Journal club

Journal club meetings are on Mondays at 5-6 pm in BCH 202.

May 1, 2017
FISH-ing for captured contacts: towards reconciling FISH and 3C

G. Fudenberg, M. Imakaev, bioRxiv (2016).

Abstract / PDF

presented by Asli

April 24, 2017
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

Justin A. Lemkul  and Alexander D. MacKerell Jr.

J. Chem. Theory Comput., Article ASAP

Abstract / PDF

 

Presented by Maciej

 

April 24, 2017
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Wang, L.-P., McKiernan, K.A., Gomes, J., Beauchamp, K.A., Head-Gordon, T., Rice, J.E., Swope, W.C., Martinez, T.J., and Pande, V.S.

J. Phys. Chem. B, Article ASAP​

Abstract / PDF 

presented by Lim

April 17, 2017
Role of Molecular Flexibility and Colloidal Descriptions of Proteins in Crowded Environments from Small-Angle Scattering

Maria Monica Castellanos, Nicholas J. Clark, Max C. Watson, Susan Krueger, Arnold McAuley, and Joseph E. Curtis

J. Phys. Chem. B, 2016, 120 (49), pp 12511–12518

Abstract / PDF

presented by Nawrocki

April 17, 2017
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

J. K. Leman, S.Lyskov and R. Bonneau
BMC Bioinformatics (2017), 18, 115

Abstract / PDF

presented by Bercem

April 10, 2017
Direct Comparison of Amino Acid and Salt Interactions with Double-Standed and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

C. T. Andrews, B. A. Campbell and A. H. Elcock, J. Chem. Theory Comput. (2017), ASAP 

Abstract / PDF

presented by Asli

March 20, 2017
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH.

J Chem Theory Comput. 2017 Feb 14;13(2):900-915.

Abstract / PDF

Missing figure

presented by Maciej

March 20, 2017
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method

T. W. Hayes and I. H. Moal

Journal of Chemical Theory and Computation (2017), 13 (3), 1401-1410.

Abstract / PDF 

presented by Lim

 

March 13, 2017
Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

C. L. Dickson, V. Hornak, R. A. Pearlstein and J. S. Duca
Journal of the American Chemical Society (2017), 139, 442-452

Abstract / PDF

presented by Bercem

March 13, 2017
Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation

N. Salvi, A. Abyzov, and M. Blackledge

J. Phys. Chem. Lett. (2016), 7, 2483-2489

Abstract / PDF

presented by Nawrocki

February 6, 2017
Compaction and segregation of sister chromatids via active loop extrusion

A. Goloborodko, M. V. Imakaev, J. F. Marko and L. Mirny, eLife (2016), 5, e14864.

Abstract / PDF

presented by Asli

January 30, 2017
The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

J. Lee, K. Joo, B. R. Brooks, and J. Lee

Journal of Chemical Theory and Computation (2015), 11, 3211.

Abstract / PDF 

presented by Lim

January 23, 2017
RNA Hairpin Folding in the Crowded Cell

M. Gao et al.
Angewandte Chemie (2016), 55, 3224-3228

Abstract / PDF

presented by Maciej

January 23, 2017
Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers

W. F. D. Bennett, C. K. Hong, Y. Wang and D. P. Tieleman
Journal of Chemical Theory and Computation (2016), 12, 4524−4533

Abstract / PDF

presented by Bercem

January 16, 2017
All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

Y. Kuroda, A. Suenaga, Y. Sato, S. Kosuda and M. Taiji

Scientific Reports (2016), 6, 19479

Abstract / PDF

presented by Nawrocki

December 19, 2016
Transferable model for chromosome architecture

M. Di Pierro, B. Zhang, E. Lieberman Aiden, P. G. Wolynes and Jose N. Onuchic, PNAS (2016), 113, 12168.

Abstract / PDF

Commentary: Three-dimensional chromosome structures from energy landscape.

G. Gursoy and J. Liang, PNAS (2016), 113, 11991.

Full Text

presented by Asli

December 5, 2016
Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

I.S. Gutierrez, F-Y Lin, K. Vanommeslaeghe, J.A. Lemkul, K.A. Armacost, C.L. Brooks III, A.D. MacKerell Jr.
Bioorganic and Medicinal Chemistry (2016), 24, 4812-4825

Abstract / PDF

presented by Bercem

November 28, 2016
Theoretical and Experimental Investigation of the Translational Diffusion of Proteins in the Vicinity of Temperature-Induced Unfolding Transition

S. Molchanov, D. A. Faizullin, and I. V. Nesmelova

J. Phys. Chem. B, 2016, 120 (39), pp 10192–10198

Abstract / PDF

presented by Nawrocki

November 21, 2016
Polymer physics of chromosome large-scale 3D organisation

A. M. Chiariello, C. Annunziatella, S. Bianco, A. Esposito and M. Nicodemi, Scientific Reports (2016), 6, 29775.

Abstract / PDF

presented by Asli

November 14, 2016
Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion

B. S. Perrin, R. W. Pastor
Biophysical Journal (2016),111,1248–1257

Abstract / PDF

presented by Bercem