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Computational Biochemistry Journal Club
Mondays at 4:00 pm we are having a journal club in BCH 402, where computational approaches
to biological questions are discussed.
Anybody interested in this area of research is welcome and encouraged
to come! The journal club is organized by Michael Feig.
Upcoming dates:
| Monday, November 23 | 4:00 PM |
| Monday, November 30 | 4:00 PM |
| Monday, December 7 | 4:00 PM |
| Monday, December 21 | 4:00 PM |
| Monday, January 4 | 4:00 PM |
| Monday, January 11 | 4:00 PM |
Recently discussed articles:
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| November 9, 2009 |
| Proc. Nat. Acad. Sci. USA |
| v. asap, p. asap |
R. Das, I. Andre, Y. Shen, Y. Wu, A. Lemak, S. Bansal, Ch. Arrowsmith, Th. Szyperski, D. Baker: Simultaneous prediction of protein folding and docking at high resolution
Abstract PDF |
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| November 2, 2009 |
| Journal of Physical Chemistry B |
| v. asap, p. asap |
C. G. Ji, J. Z. H. Zhang: Electronic Polarization is Important in Stabilizing the Native Structures of Proteins
Abstract PDF |
| Biophysical Journal |
| v. 97, p. 1917-1925 |
H.D. Herce, A. E. Garcia, J. Litt, R. S. Kane, P. Martin, N. Enrique, A. Rebolledo, V. Milesi: Arginine-Rich Peptides Destabilize the Plasma Membrane, Consistent with a Pore Formation Translocation Mechanism of Cell-Penetrating Peptides
Abstract PDF |
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| October 19, 2009 |
| Biophysical Journal |
| v. 97, p. 1168-1177 |
Y. Miller, B. Ma, R. Nussinov: Polymorphism of Alzheimer's Abeta17-42 (p3) Oligomers: The Importance of the Turn Location and Its Conformation
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. asap, p. asap |
M. D'Abramo, T. Meyer, P. Bernado, C. Pons, J. Fernandez Recio, M. Orozco: On the Use of Low-Resolution Data to Improve Structure Prediction of Proteins and Protein Complexes
Abstract PDF |
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| October 12, 2009 |
| Bulletin of the Korean Chemical Society |
| v. 30, p. 1139-1142 |
J. Jee, H.-C. Ahn: Refinement of Protein NMR Structure under Membrane-like Environments with an Implicit Solvent Model
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 5, p. 2531-2543 |
X. Periole, M. Cavalli, S.-J. Marrink, M. Ceruso: Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
Abstract PDF |
| v. asap, p. asap |
K. Song, A. Campbell, C. Bergonzo, C. de los Santos, A. Grollman, C. Simmerling: An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
Abstract PDF |
| Proteins |
| v. 77, p. 220-234 |
T. Liu, J. Horst, R. Samudarala: A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction
Abstract PDF |
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| October 5, 2009 |
| Journal of Chemical Theory and Computation |
| v. 5, p. 2202-2205 |
J. Ulmschneider, J. Doux, J. A. Killian, J. C. Smith, M. B. Ulmschneider: Peptide Partitioning and Folding into Lipid Bilayers
Abstract PDF |
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| September 28, 2009 |
| Journal of Chemical Theory and Computation |
| v. 5, p. 2465-2471 |
B. Hall, M. Sansom: Coarse-Grained MD Simulations and ProteinProtein Interactions: The CohesinDockerin System
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 106, p. 15684-15689 |
A. Johansson, E. Lindahl: Protein contents in biological membranes can explain abnormal solvation of charged and polar residues
Abstract PDF |
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| August 31, 2009 |
| Journal of Physical Chemistry B |
| v. 113, p. 11702-11709 |
W. Zheng, M. Andrec, E. Gallicchio, R. M. Levy: Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics
Abstract PDF |
| Journal of Chemical Physics |
| v. 130, p. 235106 |
T. Bereau, M. Deserno: Generic coarse-grained model for protein folding and aggregation
Abstract PDF |
| v. 130, p. 195103 |
M. Betancourt, S. Omovie: Pairwise energies for polypeptide coarse-grained models derived from atomic force fields
Abstract PDF |
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| July 20, 2009 |
| Proteins |
| v. 76, p. 837-851 |
A. Shehu, L. Kavraki, C. Clementi: Multiscale characterization of protein conformational ensembles
Abstract PDF |
| Journal of Physical Chemistry B |
| v. asap, p. asap |
P. L. Silvestrelli: Are There Immobilized Water Molecules around Hydrophobic Groups? Aqueous Solvation of Methanol from First Principles
Abstract PDF |
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| July 13, 2009 |
| Nucleic Acids Research |
| v. asap, p. asap |
G. Randall, L. Zechiedrich, B. Montgomery Pettitt: In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. asap, p. asap |
A. Ballard, C. Jarzynski: Replica exchange with nonequilibrium switches
Abstract PDF |
| Journal of the American Chemical Society |
| v. 131, p. 3438-3439 |
N. Miyashita, J. E. Straub, D. Thirumalai, Y. Sugita: Transmembrane Structures of Amyloid Precursor Protein Dimer Predicted by Replica-Exchange Molecular Dynamics Simulations
Abstract PDF |
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| June 22, 2009 |
| Biophysical Journal |
| v. 96, p. 4349-4362 |
C. Miller, S. Gellman, N. Abbott, J. de Pablo: Association of Helical b-Peptides and their Aggregation Behavior from the Potential of Mean Force in Explicit Solvent
Abstract PDF |
| Physical Review Letters |
| v. 96, p. 028105 |
E. Lyman, F. Ytreberg, D. Zuckeran: Resolution Exchange Simulation
Abstract PDF |
| Journal of Chemical Physics |
| v. 129, p. 114103 |
P. Liu, Q. Shi, E. Lyman, G. Voth: Reconstructing atomistic detail for coarse-grained models with resolution exchange
Abstract PDF |
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| June 8, 2009 |
| Biophysical Journal |
| v. 96, p. 4349-4362 |
C. Miller, S. Gellman, N. Abbott, J. de Pablo: Association of Helical beta-Peptides and their Aggregation Behavior from the Potential of Mean Force in Explicit Solvent
Abstract PDF |
| v. 96, p. 3772-3780 |
P. Freddolino, S. Park, B. Roux, K. Schulten: Force Field Bias in Protein Folding Simulations
Abstract PDF |
| Journal of Physical Chemistry B |
| v. ASAP, p. ASAP |
S. Qin, Z. Yu, Y. Yu: Structural Characterization on the Gel to Liquid-Crystal Phase Transition of Fully Hydrated DSPC and DSPE Bilayers
Abstract PDF |
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| June 1, 2009 |
| Journal of Physical Chemistry B |
| v. ASAP, p. ASAP |
E. Purisima, T. Sulea: Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies
Abstract PDF |
| Proteins |
| v. 59, p. 783-790 |
H. Nymeyer, T. Woolf, A. Garcia: Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 105, p. 6290-6295 |
D. Jiao, P. Golubkov, T. Darden, P. Ren: Calculation of protein-ligand binding free energy by using a polarizable potential
Abstract PDF |
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| May 18, 2009 |
| Biophysical Journal |
| v. 96, p. 785-797 |
Charles H. Davis, Max L. Berkowitz: Interaction Between Amyloid beta (1-42) Peptide and Phospholipid Bilayers: A Molecular Dynamics Study
Abstract PDF |
| Proteins |
| v. 76, p. 13-29 |
Julia Koehler, Nils Woetzel, Rene Staritzbichler, Charles R. Sanders, Jens Meiler: A unified hydrophobicity scale for multispan membrane proteins
Abstract PDF |
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| May 11, 2009 |
| Trends in Biochemical Sciences |
| v. 33, p. 91-100 |
H. Jang, J. Zheng, R. Nussinov: New structures help the modeling of toxic amyloidbeta ion channels
Abstract PDF |
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| May 4, 2009 |
| Nucleic Acids Research |
| v. asap, p. asap |
J. Curuksu, M. Zacharias, R. Lavery, K. Zakrzewska: Local and global effects of strong DNA bending induced during molecular dynamics simulations
Abstract PDF |
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| April 27, 2009 |
| Proteins |
| v. 75, p. 954-963 |
Yan Lu, Philippe Derreumaux, Zhi Guo, Normand Mousseau, Guanghong Wei: Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Abstract PDF |
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| April 20, 2009 |
| Journal of Physical Chemistry B |
| v. 113, p. 4664-4673 |
P. Maragakis, A. van der Vaart, M. Karplus: Gaussian-Mixture Umbrella Sampling
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 5, p. 919-930 |
D. Shivakumar, Y. Deng, B. Roux: Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model
Abstract PDF |
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| April 13, 2009 |
| Journal of Physical Chemistry B |
| v. ASAP, p. |
Soonmin Jang, Jian-Min Yuan, Jungho Shin, Thomas J. Measey, Reinhard Schweitzer-Stenner and Feng-Yin Lii: Energy Landscapes Associated with the Self-Aggregation of an Alanine-Based Oligopeptide (AAKA)4
Abstract PDF |
| Proteins |
| v. 75, p. 586-597 |
J. Ulmschneider, M. Ulmschneider: Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations
Abstract PDF |
| Nature Methods |
| v. 6, p. 3-4 |
A. Benedix, C. Becker, B. de Groot, A. Caflisch, R. Boeckmann: Predicting free energy changes using structural ensembles
Abstract PDF |
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| April 6, 2009 |
| Journal of Chemical Theory and Computation |
| v. ASAP, p. |
Hideaki Fujitani, Azuma Matsuura, Sino Sakai, Hiroyuki Sato and Yoshiaki Tanida: High-Level ab initio Calculations To Improve Protein Backbone Dihedral Parameters
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 106, p. 3776-3781 |
S. Yang, N. Banavali, B. Roux: Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
Abstract PDF |
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| March 30, 2009 |
| Biophysical Journal |
| v. 96, p. 875-886 |
G. Bellesia, J.-E. Shea: What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 5, p. 459-467 |
W. Xie, M. Orozco, D. Truhlar, J. Gao: X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water
Abstract PDF |
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| March 23, 2009 |
| Nucleic Acids Research |
| v. 36, p. 4941-4955 |
C. Mura, J. Andrew McCammon: Molecular dynamics of a kB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation
Abstract PDF |
| Biophysical Journal |
| v. 96, p. 2278-2288 |
A. Suenaga, M. Hatakeyama, A. Kiyatkin, R. Radhakrishnan, M. Taiji, B. Kholodenko: Molecular Dynamics Simulations Reveal that Tyr-317 Phosphorylation Reduces Shc Binding Affinity for Phosphotyrosyl Residues of Epidermal Growth Factor Receptor
Abstract PDF |
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| March 16, 2009 |
| Biophysical Journal |
| v. 95, p. L07-L09 |
R. Best, N.-V. Buchete: G. Hummer
Abstract PDF |
| Proteins |
| v. asap, p. asap |
P. Majek, R. Elber: A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
Abstract PDF |
| Journal of Physical Chemistry B |
| v. 113, p. 3218-3226 |
S. Muff, A. Caflisch: ETNA: Equilibrium Transitions Network and Arrhenius Equation for Extracting Folding Kinetics from REMD Simulations
Abstract PDF |
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| February 23, 2009 |
| Journal of Chemical Theory and Computation |
| v. 5, p. 422-429 |
S. Wong, R. Amaro, J. A. McCammon: MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 106, p. 2104-2109 |
S. Tripathi, J. Portman: Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin
Abstract PDF |
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| February 16, 2009 |
| Proc. Nat. Acad. Sci. USA |
| v. 105, p. 8004-8007 |
S. Mohanty, J. Meinke, O. Zimmermann, U. Hansmann: Simulation of Top7-CFr: A transient helix extension guides folding
Abstract PDF |
| Biophysical Journal |
| v. 96, p. 385-402 |
J. E. Davis, O. Rahaman, S. Patel: Molecular Dynamics Simulations of a DMPC Bilayer Using Nonadditive Interaction Models
Abstract PDF |
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| February 2, 2009 |
| Journal of Physical Chemistry B |
| v. 112, p. 6131-6136 |
L. C. Oliveira, A. Schug, J. N. Onuchic: Geometrical Features of the Protein Folding Mechanism are a Robust Property of the Energy Landscape: A Detailed Investigation of Several Reduced Models
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 106, p. 73-78 |
Naoto Hori, George Chikenji, R. Stephen Berry, Shoji Takada: Folding energy landscape and network dynamics of small globular proteins
Abstract PDF |
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| January 26, 2009 |
| Proteins |
| v. 74, p. 603-611 |
Szilvia Szep, Sheldon Park, Eric Boder, Gregory Van Duyne, Jeffery Saven: Structural coupling between FKBP12 and buried water
Abstract PDF |
| Biochemistry |
| v. 47, p. 12104-12107 |
Nathan Schmid, Christine Bollinger, Lorna Smith, Wilfred van Gunsteren: Disulfide Bond Shuffling in Bovine alpha-Lactalbumin: MD Simulation Confirms Experiment
Abstract PDF |
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| January 19, 2009 |
| Proteins |
| v. 74, p. 760-776 |
Adam D. Schuyler, Robert L. Jernigan, Pradman K. Qasba, Boopathy Ramakrishnan, Gregory S. Chirikjian: Iterative cluster-NMA: A tool for generating conformational transitions in proteins
Abstract PDF |
| v. 74, p. 682-700 |
Qingyi Yang, Kim A. Sharp: Building alternate protein structures using the elastic network model
Abstract PDF |
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| January 12, 2009 |
| Biophysical Journal |
| v. 95, p. 5862-5873 |
Nigar Kantarci-Carsibasi, Turkan Haliloglu, Pemra Doruker: Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 105, p. 20239-20244 |
G. Chopra, C. Summa, M. Levitt: Solvent dramatically affects protein structure refinement
Abstract PDF |
| Journal of Physical Chemistry B |
| v. ASAP, p. ASAP |
A. Polyansky, P. Volynsky, A. Arseniev, R. Efremov: Adaptation of a Membrane-active Peptide to Heterogeneous Environment. I. Structural Plasticity of the Peptide
Abstract PDF |
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| December 15, 2008 |
| Biophysical Journal |
| v. 95, p. 5073-5083 |
Zhiyong Zhang, Lanyuan Lu, Will G. Noid, Vinod Krishna, Jim Pfaendtner, and Gregory A. Voth: A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 4, p. 2001-2010 |
Agusti Emperador, Tim Meyer and Modesto Orozco : United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials
Abstract PDF |
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| December 1, 2008 |
| Biophysical Journal |
| v. 95, p. 5030-5036 |
G. Wieczorek, P. Zielenkiewicz: Influence of Macromolecular Crowding on Protein-Protein Association Rates¿a Brownian Dynamics Study
Abstract PDF |
| v. 95, p. 5021-5029 |
In-Chul Yeh, Mark A. Olson, Michael S. Lee, and Anders Wallqvist: Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane Peptide from Influenza A Virus
Abstract PDF |
| v. 95, p. 5100-5110 |
Po-Chao Wen and Emad Tajkhorshid: Dimer Opening of the Nucleotide Binding Domains of ABC Transporters after ATP Hydrolysis
Abstract PDF |
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| November 24, 2008 |
| Proc. Nat. Acad. Sci. USA |
| v. 105, p. 13877-13882 |
M. Roca, B. Messer, D. Hilvert, A. Warshel: On the relationship between folding and chemical landscapes in enzyme catalysis
Abstract PDF |
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| November 10, 2008 |
| Biophysical Journal |
| v. 94, p. 550-561 |
A. Vargiu, P. Ruggerone, A. Magistrato, P. Carloni: Sliding of Alkylating Anticancer Drugs along the Minor Groove of DNA: New Insights on Sequence Selectivity
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 4, p. 1733-1744 |
H. Tjong, H.-X. Zhou: Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method
Abstract PDF |
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| October 27, 2008 |
| Biophysical Journal |
| v. 95, p. L57-L59 |
R. Hills, C. Brooks: Coevolution of Function and the Folding Landscape: Correlation with Density of Native Contacts
Abstract PDF |
| Protein Science |
| v. 17, p. 1576-1585 |
M. Lu, A. Dousis, J. Ma: OPUS-Rota: A fast and accurate method for side-chain modeling
Abstract PDF |
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| October 20, 2008 |
| Journal of Chemical Theory and Computation |
| v. 4, p. 1119-1128 |
M. Abraham, J. Gready: Ensuring Mixing Efficiency of Replica Exchange Molecular Dynamics Simulations
Abstract PDF |
| Journal of Chemical Physics |
| v. 127, p. 145104 |
E. Kim, S. Jang, Y. Pak: Consistent free enery landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation
Abstract PDF |
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| October 6, 2008 |
| Journal of Chemical Theory and Computation |
| v. ASAP, p. ? |
M. Ulmschneider, J. Ulmschneider: Folding Peptides into Lipid Bilayer Membranes
Abstract PDF |
| v. ASAP, p. ? |
D. Cerrutti, R. Duker, P. Freddolino, H. Fan, T. Lybrand: A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics
Abstract PDF |
| Nucleic Acids Research |
| v. 36, p. 5645-5651 |
G. Chillemi, I. D'Annessa, P. Fiorani, C. Losasso, P. Benedetti, A. Desideri: Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations
Abstract PDF |
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| September 29, 2008 |
| Biophysical Journal |
| v. 95, p. 3575-3590 |
M. A. Cuendet, O. Michielin: Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex
Abstract PDF |
| Journal of Physical Chemistry B |
| v. 111, p. 1416-1423 |
M. Hagen, B. Kim, P. Liu, R. A. Friesner, B. J. Berne: Serial Replica Exchange
Abstract PDF |
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| September 22, 2008 |
| Journal of Chemical Theory and Computation |
| v. 4, p. 1348 |
C. Xu, J. Wang, H. Liu: A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations
Abstract PDF |
| Proc. Nat. Acad. Sci. USA |
| v. 104, p. 11963-11968 |
P. Alexander, Y. He, Y. Chen, J. Orban, P. Bryan: The design and characterization of two proteins with 88% sequence identity but different structure and function
Abstract PDF |
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| September 15, 2008 |
| Journal of Chemical Theory and Computation |
| v. 4, p. 657-672 |
B. Strodel, D. Wales: Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide
Abstract PDF |
| Biophysical Journal |
| v. 94, p. 1185-1193 |
H. Nymeyer, H.-X. Zhou: A method to Determine Dielectric Constants in Nonhomogeneous Systems
Abstract PDF |
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| September 9, 2008 |
| Proc. Nat. Acad. Sci. USA |
| v. 105, p. 12259-12264 |
D. Beck, D. Alonso, D. Inoyama, V. Daggett: The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
Abstract PDF |
| BMC Structural Biology |
| v. 8, p. 31 |
S. Chakravarty, S. Godbole, B. Zhang, S. Berger, R. Sanchez: Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure
Abstract PDF |
| Biophysical Journal |
| v. 95, p. 2647-2657 |
H. Wang, J. de Joannis, Y. Jiang, J. Gaulding, B. Albrect, F. Yin, K. Khanna, J. Kindt: Bilayer Edge and Curvature Effects on Partitioning of Lipids by Tail Length: Atomistic Simulations
Abstract PDF |
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| August 25, 2008 |
| BMC Structural Biology |
| v. 8, p. 18 |
J. Cheng: A multi-template combination algorithm for protein comparative modeling
Abstract PDF |
| Proteins |
| v. 72, p. 1171-1188 |
J. Zhu, H. Fan, X. Periole, B. Honig, A. Mark: Refining homology models by combining replica-exchange molecular dynamics and statistical potentials
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 4, p. 1516-1525 |
C. de Oliveira, D. Hamelberg, J. A. McCammon: Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
Abstract PDF |
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| August 11, 2008 |
| Journal of Chemical Theory and Computation |
| v. 4, p. 819-834 |
L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D. P. Tieleman, S.-J. Marrink: The MARTINI Coarse-Grained Force Field: Extension to Proteins
Abstract PDF |
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| July 28, 2008 |
| Proteins |
| v. 72, p. 299-312 |
H. Jang, N. Michaud-Agrawal, J. Johnston, T. Woolf: How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers
Abstract PDF |
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| May 5, 2008 |
| Journal of Computational Chemistry |
| v. 29, p. 1460-1465 |
P. Rotkiewicz, J. Skolnick: Fast Procedure for Reconstruction of Full-Atom Protein Models from Reduced Representations
Abstract PDF |
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| April 21, 2008 |
| Biophysical Journal |
| v. 94, p. 3227-3240 |
L. Wroblweska, A. Jagielska, J. Skolnick: Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models
Abstract PDF |
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| March 17, 2008 |
| Journal of Chemical Theory and Computation |
| v. 4, p. 515-521 |
M. S. Lin, T. Head-Gordon: Improved Energy Selection of Nativelike Protein Loops from Loop Decoys
Abstract PDF |
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| March 10, 2008 |
| Structure |
| v. 15, p. 1482-1492 |
D. Seeliger, J. Haas, B. de Groot: Geometry-Based Sampling of Conformational Transitions in Proteins
Abstract PDF |
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| February 21, 2008 |
| Proc. Nat. Acad. Sci. USA |
| v. 104, p. 17674-17679 |
A. Schug, P. C. Whitford, Y. Levy, J. N. Onuchic: Mutations as trapdoors to two competing native conformations of the Rop-dimer
Abstract PDF |
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| January 21, 2008 |
| Proteins |
| v. 70, p. 731-738 |
Mao-Cai Yan, Yu Sha, Jian Wang, Xu-Qiong Xiong, Jin-Hong Ren, Mao-Sheng Cheng: Molecular dynamics simulations of HIV-1 protease monomer: Assembly of N-terminus and C-terminus into beta-sheet in water solution
Abstract PDF |
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| January 7, 2008 |
| Journal of Physical Chemistry B |
| v. ?, p. ? |
D. Mobley, Ken Dill, J. Chodera: Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules
Abstract PDF |
| Biophysical Journal |
| v. 94, p. 71 |
Marilisa Neri, Marc Baaden, Vincenzo Carnevale, Claudio Anselmi, Amos Maritan, and Paolo Carloni: Microseconds Dynamics Simulations of the Outer-Membrane Protease T
Abstract PDF |
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| November 26, 2007 |
| Protein Science |
| v. 16, p. 2716 |
S. Lorenzen, Y. Zhang: Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 3, p. 2146 |
W. Han, Y.-D. Wu: Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides
Abstract PDF |
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| November 12, 2007 |
| Journal of the American Chemical Society |
| v. ASAP, p. ASAP |
A. Perez, J. Luque, M. Orozco: Dynamics of B-DNA on the Microsecond Time Scale
Abstract PDF |
| Biophysical Journal |
| v. 93, p. 3382 |
D. Beck, V. Daggett: A One-Dimensional Reaction Coordinate for Identification of Transition States from Explicit Solvent Pfold-Like Calculations
Abstract PDF |
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| November 5, 2007 |
| Journal of the American Chemical Society |
| v. 129, p. 13537 |
Yongmei Pan, Daquan Gao, Wenchao Yang, Hoon Cho, and Chang-Guo Zhan: Free Energy Perturbation (FEP) Simulation on the Transition States of Cocaine Hydrolysis Catalyzed by Human Butyrylcholinesterase and Its Mutants
Abstract PDF |
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| October 29, 2007 |
| Biophysical Journal |
| v. 93, p. 3156 |
Jochen S. Hub, Tim Salditt, Maikel C. Rheinstädter, and Bert L. de Groot: Short-Range Order and Collective Dynamics of DMPC Bilayers: A Comparison between Molecular Dynamics Simulations, X-Ray, and Neutron Scattering Experiments
Abstract PDF |
| Journal of Chemical Theory and Computation |
| v. 3, p. 1550 |
D. R. Nutt, J. C. Smith: Molecular Dynamics Simulation of Proteins: Can the explicit water model be varied?
Abstract PDF |
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| October 22, 2007 |
| Journal of Physical Chemistry B |
| v. 111, p. 12263 |
Chunhu Tan, Yu-Hong Tan, and Ray Luo: Implicit Nonpolar Solvent Models
Abstract PDF |
| Journal of Molecular Biology |
| v. 373, p. 1123 |
Shantanu Sharma, Peng Gong, Brenda Temple, Debadeep Bhattacharyya, Nikolay V. Dokholyan and Stephen G. Chaney: Molecular Dynamic Simulations of Cisplatin- and Oxaliplatin-d(GG) Intrastand Cross-links Reveal Differences in their Conformational Dynamics
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| October 15, 2007 |
| Journal of Chemical Theory and Computation |
| v. 3, p. 1867 |
F. Pizzitutti, M. Marchi, D. Borgis: Coarse-Graining the Accessible Surface and the Electrostatics of Proteins for Protein-Protein Interactions
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| Journal of Computational Chemistry |
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U. Haberthuer, A. Caflisch: FACTS: Fast Analytical Continuum Treatment of Solvation
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| Proteins |
| v. 69, p. 297 |
J.P. Ulmschneider, M.B. Ulmschneider, and A. Di Nola: Monte Carlo folding of trans-membrane helical peptides in an implicit generalized born membrane
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| September 10, 2007 |
| Journal of Molecular Biology |
| v. 371, p. 1354 |
T. Oroguchi, M. Ikeguchi, M. Ota, K. Kuwajima, and A. Kidera: Unfolding pathways of goat alpha-Lactalbumin as revealed in multiple alignment of molecular dynamics trajectories
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| Proteins |
| v. 69, p. 394 |
J. Maupetit, P. Tuffery, and P. Derreumaux: A coarse-grained protein force field for folding and structure prediction
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| August 27, 2007 |
| Journal of Physical Chemistry B |
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N. Basdevant, D. Borgis, and T. Ha-Duong: A Coarse-Grained Protein-Protein Potential Derived from an All-Atom Force Field
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| July 30, 2007 |
| Proteins |
| v. 68, p. 646 |
Allison P. Heath,Lydia E. Kavraki, and Cecilia Clementi: From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
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| July 16, 2007 |
| Journal of Computational Chemistry |
| v. 28, p. 2051 |
Balazas Jojart, and Tomas A. Martinek: Performance of the General Amber Force Field in Modeing Aqueous POPC Membrane Bilayers
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| July 9, 2007 |
| Journal of Computational Chemistry |
| v. 28, p. 2059 |
Liliana Wroblewska, Jeffrey Skolnick: Can a Physicis-Based, All-Atom Potentiali Find a Protein's Native Structure Among Misfolded Structures? I. Large Scale AMBER Benchmarking
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| IEEE/ACM Transactions on Computational Biology and Bioinformatics |
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Nils Weskamp, Eyke Hullermeier, Daniel Kuhn, and Gerhard Klebe: Multiple Graph Alignment for Structural Analysis of Protein Active Sites
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| July 2, 2007 |
| Proteins |
| v. 68, p. 581 |
Mary Hongying, Michael Cascio, and Rob D. Coalson: Homology Modeling and Molecular Dynamics Simulations of the Alpha1 Glycine Receptor Reveals Different States of the Channel
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| June 25, 2007 |
| Structure |
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Matthew S. Lin, NIcolas Lux Fawi, and Teresa Head-Gordon: Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction
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| Journal of Chemical Physics |
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Mikael Lund, Bo Jonsson, and Clifford E. Woodward: Implications of High Dielectric Constant in Proteins
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| June 4, 2007 |
| Journal of Physical Chemistry B |
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Alessandra Villa, Hao Fan, Tsjerk Wassenaar, and Alan E. Mark: How sensitive Are Nanosecond Molecular Dynamics Simulations of Proteins to changes in the Force Field?
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| Proteins |
| v. 68, p. 243 |
Andrej Perdih, Miha Kotnik, Milan Hodoscek, and Tom Solmajer: Trageted Molecular Dynamics Simulation Studies of Binding and Conformational Changes in E.coli MurD
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| Biophysical Journal |
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Marcus B. Kubitzki and Bert L. de Groot: Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange
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| May 21, 2007 |
| Biophysical Journal |
| v. 92, p. 2338 |
Martin B. Ulmschneider, Jacob P. Ulmschneider, Martin S. P. Sansom, and Alfredo Di Nola: A Generalized Born Implicit-Membrane Representation Compared to Experimental Insertion Free Energies
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| May 7, 2007 |
| Biophysical Journal |
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Gary S. Ayton, Philip D. Blood and Gregory A. Voth: Membrane Remodeling from N-BAR Domain Interactions:Insights from Multi-Scale Simulation
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| Journal of Physical Chemistry B |
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Stefano Piana and Alessandro Laio: A Bias-Echange Approch to protein Folding
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Jason E. Donald, William W. Chen and Eugene I. Shakhnowich: Energetics of Protein-DNA Interactions
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| Biophysical Journal |
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Dana Doucet, Adrian Roitberg, and Stephen J. Hagen: Kinetics of Internal-Loop Formation in Polypeptide Chains:A Simulation Study
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| Biophysical Journal |
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Ivan Coluzza and Daan Frenkel: Monte Carlo Study of Substrate-Induced Folding and Refolding of Lattice Proteins
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| Journal of Physical Chemistry B |
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Wely B. Floriano, Gilberto B. Domont, and Marco A.C. Nascimento: A Molecular Dynamics Study of the Correlations between Solvent-Accesible Surface, Molecular Volume, and Folding State
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| Biophysical Journal |
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Lintao Bu, Wonpil Im, and Charles L. Brooks III: Membrane Assembly of Simple helix Homo-Oligomers Studied via Molecular Dynamics Simulations
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| December 18, 2006 |
| Biophysical Journal |
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Dmitry A. Kondrashov, Qiang Cui, and George N. Phillips, Jr.: Optimization and Evaluation of a Coarse-Grained Model of Protein Motion Using X-Ray Crystal Data
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| Structure |
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Filip Lanka¿, Richard Lavery, and John H. Maddocks: Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles
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| Journal of Chemical Information and Modeling |
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Ákos Papp, Anna Gulyás-Forró, Zsolt Gulyás, György Dormán, László Ürge, and Ferenc Darvas: Explicit Diversity Index (EDI): A Novel Measure for Assessing the Diversity of Compound Databases
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| Proteins |
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Jens Meiler, David Baker: ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
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| November 6, 2006 |
| Journal of Computational Chemistry |
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Peter C. Anderson, Sandro Mecozzi: Minimum sequence requirements for selective RNA-ligand binding: A molecular mechanics algorithm using molecular dynamics and free-energy techniques
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| October 30, 2006 |
| Journal of Computational Chemistry |
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Oliver F. Lange, Lars V. Schäfer, Helmut Grubmüller: Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
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| Journal of Chemical Information and Modeling |
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Yoshifumi Fukunishi, Satoru Kubota, and Haruki Nakamura: Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening
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| Journal of Physical Chemistry B |
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Jakob P. Ulmschneider, Martin B. Ulmschneider, and Alfredo Di Nola: Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations
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| Protein Science |
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Patrick J. Fleming, Haipeng Gong, and George D. Rose: Secondary structure determines protein topology
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E. Zaslavsky, M. Singh: A combinatorial optimization approach for diverse motif finding applications
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| Journal of Physical Chemistry B |
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Pu Liu, Xuhui Huang, Ruhong Zhou, and B. J. Berne: Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent
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R.F.S. Walters, W. F. DeGrado: Helix-packing motifs in membrane proteins
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| Journal of Physical Chemistry B |
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Lijiang Yang, Chun-hu Tan, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Piotr Cieplak, James Caldwell, Peter A. Kollman, and Ray Luo: New-Generation Amber United-Atom Force Field
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| April 17, 2006 |
| Journal of Chemical Information and Modeling |
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J. Christian Baber, William A. Shirley, Yinghong Gao, and Miklos Feher: The Use of Consensus Scoring in Ligand-Based Virtual Screening
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Meir Glick, Jeremy L. Jenkins, James H. Nettles, Hamilton Hitchings, and John W. Davies: Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers
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| Proteins |
| v. 63, p. 644 |
Brajesh K. Rai, András Fiser: Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling
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| Journal of Chemical Theory and Computation |
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Roman Affentranger, Ivano Tavernelli, and Ernesto E. Di Iorio: A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling
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| Protein Science |
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Hao Fan and Alan E. Mark: Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures
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| Journal of Chemical Theory and Computation |
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Alexey L. Kaledin, Martina Kaledin, and Joel M. Bowman: All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method
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Yelena A. Arnautova, Anna Jagielska, and Harold A. Scheraga: A New Force Field (ECEPP-05) for Peptides, Proteins, and Organic Molecules
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| Proteins |
| v. 63, p. 278 |
David Schell, Jerry Tsai, J. Martin Scholtz, C. Nick Pace: Hydrogen bonding increases packing density in the protein interior
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| Bioinformatics |
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Jean-Christophe Gelly, Alexandre G. de Brevern, and Serge Hazout: 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
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| Biochemistry |
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Ozge Kurkcuoglu, Robert L. Jernigan, and Pemra Doruker: Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks
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| Biophysical Journal |
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Paula Petrone and Vijay S. Pande: Can Conformational Change Be Described by Only a Few Normal Modes?
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| February 27, 2006 |
| Journal of Chemical Theory and Computation |
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R. Geney, M. Layten, R. Gomperts, V. Hornak, C. Simmerling: Investigation of Salt Bridge Stability in a Generalized Born Solvent Model
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| Journal of Molecular Biology |
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Y. Kong, J. Ma, M. Karplus, W. Lipscomb: The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis
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R. Rohs, I. Bloch, H. Sklenar, Z. Shakked: Molecular flexibility in ab initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations
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| Proteins |
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Z. Zhang, M. Grigorov: Similarity networks of protein binding sites
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| Journal of Computational Chemistry |
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Z. Yu, M. Jacobson, R. Friesner: What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules
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| Biophysical Journal |
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N. Strickland, A. Mulholland, J. Harvey: The Fe-CO Bond Energy in Myoglobin: A QM/MM Study of the Effect of Tertiary Structure
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| Journal of Chemical Theory and Computation |
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R. Rizzo, T. Aynechi, D. Case, I. Kuntz: Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions
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| January 30, 2006 |
| Journal of Chemical Information and Modeling |
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R. Sathyapriya, K. Brinda, S. Vishveshwara: Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures
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S. Cho, Y. Sun: FLAME: A Program to Flexibly Align Molecules
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T. Lassmann, E. Sonnhammer: Automatic assessment of alignment quality
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O. Gonzalez-Amezcua, M. Hernandez-Contreras: Structural thermodynamics of lamellar cationic lipid-DNA complex: DNA compressibility modulus
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| Proteins |
| v. 62, p. 381 |
Y. Fujitsuka, G. Chikenji, S. Takada: SimFold energy function for de novo protein structure prediction: Consensus with Rosetta
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| Journal of Physical Chemistry B |
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G. Archontis, T. Simonson: A Residue-Pairwise Generalized Born Scheme Suitable for Protein Design Calculations
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H. Xu, K. Dill: Water's Hydrogen Bonds in the Hydrophobic Effect: A Simple Model
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Z. Li, T. Lazaridis: Thermodynamics of Buried Water Clusters at a Protein-Ligand Binding Interface
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S. Cheng, Y. Yang, W. Wang, H. Liu: Transition State Ensemble for the Folding of B Domain of Protein A: A Comparison of Distributed Molecular Dynamics Simulations with Experiments
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| Journal of Computational Chemistry |
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J. Hu, A. Ma, A. Dinner: Monte Carlo simulations of biomolecules: The MC module in CHARMM
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| Journal of Chemical Physics |
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J. Franklin, S. Doniach: Adaptive time stepping in biomolecular dynamics
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| Biophysical Journal |
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W. Shinoda, K. Shinoda, T. Baba, M. Mikami: Molecular Dynamics Study of Bipolar Tetraether Lipid Membranes
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Z. Yu, M. Jacobson, R. Friesner: What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules
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| Journal of Chemical Theory and Computation |
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T. Rod, U. Ryde: Accurate QM/MM Free Energy Calculations of Enzyme Reactions: Methylation by Catechol O-Methyltransferase
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| Journal of Molecular Biology |
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G. Smith, M. Sternberg, P. Bates: The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking
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| Proteins |
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A. Yan, R. Jernigan: How do side chains orient globally in protein structures?
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H. Woo, B. Roux: Chemical Theory and Computation Special Feature: Calculation of absolute protein-ligand binding free energy from computer simulations
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| Journal of Chemical Information and Modeling |
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P. Labute: On the Perception of Molecules from 3D Atomic Coordinates
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| Biophysical Journal |
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S. Maguid, S. Fernandez-Alberti, L. Ferrelli, J. Echave: Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family
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| Journal of Computational Chemistry |
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J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. Skeel, L. Kale, K. Schulten: Scalable molecular dynamics with NAMD
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| Biochemistry |
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I. Yildirim, D. Turner: RNA Challenges for Computational Chemists
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| Journal of Computational Chemistry |
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David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods: The Amber biomolecular simulation programs
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S. Jha, P. Coveney, C. Laughton: Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
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| Proteins |
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J. Qiu, R. Elber: Atomically detailed potentials to recognize native and approximate protein structures
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A. Baumketner, J.-E. Shea: The Influence of Different Treatments of Electrostatic Interactions on the Thermodynamics of Folding of Peptides
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| Journal of Computational Chemistry |
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A. Macias, A. MacKerell: CH/pi interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field
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| Protein Science |
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M. Shenderovich, R. Kagan, P. Heseltine, K. Ramnarayan: Structure-based phenotyping predicts HIV-1 protease inhibitor resistance
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| Journal of Chemical Physics |
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G. Petraglio, M. Ceccarelli, M. Parrinello: Nonperiodic boundary conditions for solvated systems
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| Journal of Molecular Biology |
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N. Ota, D. Agard: Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion
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| Journal of Chemical Physics |
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T. Dirama, G. Carri, A. Sokolov: Coupling between lysozyme and glycerol dynamics: Microscopic insights from molecular-dynamics simulations
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H. Chen, H. Zhou: Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
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| Science |
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A. Korkegian, M. Black, D. Baker, B. Stoddard: Computational Thermostabilization of an Enzyme
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| Journal of Computational Chemistry |
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C. Bartels, A. Widmer, C. Ehrhardt: Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations
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| Biophysical Journal |
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Y. Sugita, Y. Okamoto: Molecular Mechanism for Stabilizing a Short Helical Peptide Studied by Generalized-Ensemble Simulations with Explicit Solvent
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| Journal of Computational Chemistry |
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S. Höfinger: Solving the Poisson-Boltzmann equation with the specialized computer chip MD-GRAPE-2
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| Journal of Chemical Physics |
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B. Lu, D. Zhang, J. McCammon: Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method
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D. Sundholm: Universal method for computation of electrostatic potentials
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| Journal of Molecular Biology |
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J. Lipfert, J. Franklin, F. Wu, S. Doniach: Protein Misfolding and Amyloid Formation for the Peptide GNNQQNY from Yeast Prion Protein Sup35: Simulation by Reaction Path Annealing
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| Journal of Molecular Biology |
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M. Roy, L. Chavez, J. Finke, D. Heidary, J. Onuchic, P. Jennings: The Native Energy Landscape for Interleukin-1¿. Modulation of the Population Ensemble through Native-state Topology
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| Protein Science |
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S. Marshall, C. Vizcarra, S. Mayo: One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations
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| Journal of the American Chemical Society |
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D. Sakharov and C. Lim: Zn Protein Simulations Including Charge Transfer and Local Polarization Effects
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| Journal of Medicinal Chemistry |
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P. Hajduk, J. Huth, S. Fesik: Druggability Indices for Protein Targets Derived from NMR-Based Screening Data
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| Biophysical Journal |
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M. Pickholz, L. Saiz, and M. Klein: Concentration Effects of Volatile Anesthetics on the Properties of Model Membranes: A Coarse-Grain Approach
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| Journal of Computational Chemistry |
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R. Petrella, M. Karplus: Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation
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M. Pellegrini-Calace and J. Thornton: Detecting DNA-binding helix¿turn¿helix structural motifs using sequence and structure information
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| Biochemistry |
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H. Carstens, C. Renner, A. Milbradt, L. Moroder, P. Tavan: Multiple Loop Conformations of Peptides Predicted by Molecular Dynamics Simulations Are Compatible with Nuclear Magnetic Resonance
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| Proteins |
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C. Frenz: Neural network-based prediction of mutation-induced protein stability changes in Staphylococcal nuclease at 20 residue positions
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T. Soares, P. Huenenberger, M. Kastenholz, V. Kraeutler, T. Lenz, R. Lins, C. Oostenbrink, W. van Gunsteren: An improved nucleic acid parameter set for the GROMOS force field
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| Journal of Physical Chemistry B |
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J. Zhu, E. Alexov, B. Honig: Comparative Study of Generalized Born Models: Born Radii and Peptide Folding
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| Proteins |
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P. Crowley, A. Golovin: Cation-Pi interactions in protein-protein interfaces
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M. Babor, H. Greenblatt, M. Edelman, V. Sobolev: Flexibility of metal binding sites in proteins on a database scale
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E. Sorin, V. Pande: Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling
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| Journal of Physical Chemistry B |
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C. Margulis: Computational Study of the Dynamics of Mannose Disaccharides Free in Solution and Bound to the Potent Anti-HIV Virucidal Protein Cyanovirin
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| Biophysical Journal |
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M. Venturoli, B. Smit, M. Sperotto: Simulation Studies of Protein-Induced Bilayer Deformations, and Lipid-Induced Protein Tilting, on a Mesoscopic Model for Lipid Bilayers with Embedded Proteins
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B. Liu, J. Zhou: SARS-CoV protease inhibitors design using virtual screening method from natural products libraries
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C. Saunders, D. Baker: Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design
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| Proteins |
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D. Sengupta, L. Meinhold, D. Langosch, G. Ullmann, J. Smith: Understanding the energetics of helical peptide orientation in membranes
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A. Gutteridge, J. Thornton: Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
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R. Prabhakar, K. Morokuma, D. Musaev: A comparative study of various computational approaches in calculating the structure of pyridoxal 5-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment
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| Journal of the American Chemical Society |
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Y.Cheng, Y. Zhang, J. McCammon: How Does the cAMP-Dependent Protein Kinase Catalyze the Phosphorylation Reaction: An ab Initio QM/MM Study
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S. Chakravarty, L. Wang, R. Sanchez: Accuracy of structure-derived properties in simple comparative models of protein structures
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C. Kalyanaraman, K. Bernacki, M. Jacobson: Virtual Screening against Highly Charged Active Sites: Identifying Substrates of Alpha-Beta Barrel Enzymes
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H. Refsgaard, B. Jensen, P. Brockhoff, S. Padkkjaer, M. Guldbrandt, M. Christensen: In Silico Prediction of Membrane Permeability from Calculated Molecular Parameters
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J. Dolenc, C. Oostenbrink, J. Koller, W. van Gunsteren: Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
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E. Granseth, G. von Heijne, A. Elofsson: A Study of the Membrane%G–%@Water Interface Region of Membrane Proteins
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A. Jaramillo, S. Wodak: Computational Protein Design Is a Challenge for Implicit Solvation Models
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E. Bindewald, J. Skolnick: A scoring function for docking ligands to low-resolution protein structures
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S. Dixit, F. Pitici, D. Beveridge: Structure and axis curvature in two dA6·dT6 DNA oligonucleotides: Comparison of molecular dynamics simulations with results from crystallography and NMR spectroscopy
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K. Lindorff-Larsen, R. Best, M. DePristo, C. Dobson, M. Vendruscolo: Simultaneous determination of protein structure and dynamics
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P. Dobson, A. Doig: Predicting Enzyme Class From Protein Structure Without Alignments
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T. Herges, W. Wenzel: An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins
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T. Shiraki, T. Kodama, H. Jingami, N. Kamiya: Rational discovery of a novel interface for a coactivator in the peroxisome proliferator-activated receptor : Theoretical implications of impairment in type 2 diabetes mellitus
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E. Fadrna, N. Spackova, R. Stefl, J. Koca, T. Cheatham, J. Sponer: Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
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G. Amitai, A. Shemesh, E. Sitbon, M. Shklar, D. Netanely, I. Venger, S. Pietrokovski: Network Analysis of Protein Structures Identifies Functional Residues
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K. Lee, C. Czaplewski, S.-Y. Kim, J. Lee: An efficient molecular docking using conformational space annealing
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J. Pei, Q. Wang, J. Zhou, L. Lai: Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation
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M. Sotomayor, K. Schulten: Molecular Dynamics Study of Gating in the Mechanosensitive Channel of Small Conductance MscS
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J. Chen, W. Im, C. Brooks: Refinement of NMR Structures Using Implicit Solvent and Advanced Sampling Techniques
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X. Li, O. Keskin, B. Ma, R. Nussinov, J. Liang: Protein-Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking
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J. Mongan, D. Case, J. McCammon: Constant pH molecular dynamics in generalized Born implicit solvent
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J. Ulmschneider, W. Jorgensen: Monte Carlo Backbone Sampling for Nucleic Acids Using Concerted Rotations Including Variable Bond Angles
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W. Meisner, T. Sosnick: Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: Implications for downhill folding
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M. Fornabaio, F. Spyrakis, A. Mozzarelli, P. Cozzini, D. Abraham, G. Kellogg: Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes
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| Biopolymers |
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G. Verkhivker: Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: Hierarchy of structural loss from all-atom Monte Carlo simulations of p27Kip1 unfolding-unbinding and structural determinants of the binding mechanism
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| Proteins |
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K. Gunaseakaran, B. Ma, R. Nussinov: Is allostery an intrinsic property of all dynamic proteins?
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F. Corcho, J. Canto, J. Perez: Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics
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S. Noskov, W. Im, B. Roux: Ion Permeation through the alpha-Hemolysin Channel: Theoretical Studies Based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory
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E. Martineau, P.-J. L'Hereux, J. Gunn: Biased fragment distribution in MC simulation of protein folding
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R. Session, G. Thomas, M. Parker: Water as a Conformational Editor in Protein Folding
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C. Stultz: An Assessment of Potential of Mean Force Calculations with Implicit Solvent Models
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O. Winther, A. Krogh: Teaching computers to fold proteins
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W. L. Jorgensen, J. P. Ulmschneider, J. Tirado-Rives: Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field
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N. Smolin, R. Winter: Molecular Dynamics Simulations of Staphylococcal Nuclease: Properties of Water at the Protein Surface
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M. Lee, F. Salsbury, M. Olson: An efficient hybrid explicit/implicit solvent method for biomolecular simulations
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B. Zagrovic, V. Pande: How Does Averaging Affect Protein Structure Comparison on the Ensemble Level?
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Y. Chen, T. Kortemme, T. Robertson, D. Baker, G. Varani: A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys
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J. Havranek, C. Duarte, D. Baker: A Simple Physical Model for the Prediction and Design of Protein-DNA Interactions
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| October 4, 2004 |
| Journal of Medicinal Chemistry |
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A. Ferrari, B. Wei, L. Constantino, B. Shoichet: Soft Docking and Multiple Receptor Conformations in Virtual Screening
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| Protein Science |
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H.-H. Tsai, C.-J. Tsai, B. Ma, R. Nussinov: In silico protein design by combinatorial assembly of protein building blocks
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M. Khalili, J. A. Saunders, A. Liwo, S. Oldziej, H. A. Scheraga: A united residue force-field for calcium-protein interactions
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G. Crippen: Statistical mechanics of protein folding by cluster distance geometry
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J.-Y. Wang, S. Ahmad, M. Gromiha, A. Sarai: Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis
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R. Zhou, X. Huang, C. Margulis, B. Berne: Hydrophobic Collapse in Multidomain Protein Folding
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J. Liu, E. Luijten: Rejection-Free Geometric Cluster Algorithm for Complex Fluids
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| Proteins |
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R. Endres, T. Schulthess, N. Wingreen: Toward an Atomistic Model for Predicting Transcription-Factor Binding Sites
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C. Wilson, P. Boardman, A. Doig, S. Hubbard: Improved prediction for N-termini of alpha-helices using empirical information
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M. Lepsik, Z. Kriz, Z. Havlas: Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations
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| Biophysical Journal |
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T. Stockner, W. Ash, J. MacCallum, D. Tieleman: Direct Simulation of Transmembrane Helix Association: Role of Asparagines
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| Journal of Computational Chemistry |
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Z.-X. Wang, Y. Duan: Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (phi,psi) energy maps and conformers in the gas phase, ether, and water
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J. Michel, R. Taylor, J. Essex: The parameterization and validation of generalized born models using the pairwise descreening approximation
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