Journal club

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

November 18, 2019
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, et al. (2018) PLOS Genetics 14(12): e1007872.

Abstract / PDF

presented by Gilberto

November 4, 2019
In-Cell Protein–Protein Contacts: Transient Interactions in the Crowd

J. Phys. Chem. Lett. 2019, 10, 18, 5667-5673

Abstract / PDF

presented by Nawrocki

October 28, 2019
Three archetypical classes of macromolecular regulators of protein liquid–liquid phase separation

A. Ghosh, K. Mazarakos, and H.-X. Zhou
PNAS, 116, 19474-19483, 2019

Abstract / PDF

presented by Bercem

October 21, 2019
Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein–Protein Interaction

J. Chem. Theory Comput. 2019, 15, 4318-4331

Abstract / PDF

presented by Nawrocki

October 14, 2019
Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

Guterres, H., Lee, H. S., and Im, W., JCTC (2019).

Abstract PDF 

presented by Lim

October 14, 2019
Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes

I. Alshareedah, T. Kaur, J. Ngo, H. Seppala, L.-A. D. Kounatse, W. Wang, M. M. Moosa, and P. R. Banerjee.
J. Am. Chem. Soc., 141, 37, 2019

Abstract / PDF

presented by Bercem

October 7, 2019
Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields

J. Phys. Chem. Lett. 2018, 9, 7110-7116

Abstract / PDF

presented by Nawrocki

September 16, 2019
Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

Noé F, Olsson S, Köhler J, Wu H (2019) Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning. Science 365(6457):eaaw1147–13.

Abstract PDF 

presented by Lim

August 5, 2019
Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

D.T. McSwiggen, A.S. Hansen, S.S. Teves, H. Marie Nelly, Y. Hao, A.B. Heckert, K.K. Umemoto, C. Dugast-Darzacq, R. Tijan and X. Darzacq.
Elife, 8, e47098, 2019

Abstract

presented by Bercem

July 8, 2019
Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects

J. Chem. Theory Comput. 2019 15, 6, 3854-3867

Abstract / PDF

presented by Nawrocki

June 3, 2019
Sequence determinants of protein phase behavior from a coarse-grained model

G. L. Dignon, W. Zheng, Y. C. Kim, R. B. Best, J. Mittal
PLOS Computational Biology, 14(1): e1005941, 2018

Abstract / PDF

presented by Bercem

May 20, 2019
QRNAS: software tool for refinement of nucleic acid structures

Stasiewicz, J., Mukherjee, S., Nithin, C., & Bujnicki, J. M. (2019). QRNAS: software tool for refinement of nucleic acid structures. BMC structural biology19(1), 5.

 

Abstract / PDF

 

presented by Maciej

April 22, 2019
Intrinsic cleavage of RNA polymerase II adopts a nucleobase-independent mechanism assisted by transcript phosphate

C. K. M. Tse, J. Xu, L. Xu, F. K. Sheong, S. Wang, H. Y. Chow, X. Gao,.X. Li, P. P-H. Cheung, D. Wang, Y. Zhang and X. Huang
Nature Catalysis, 2, 228-235, 2019

Abstract / PDF

presented by Bercem

April 22, 2019
End-to-End Differentiable Learning of Protein Structure

AlQuraishi M (2019) End-to-End Differentiable Learning of Protein Structure. Cell Syst. doi:10.1016/j.cels.2019.03.006. (Available online Apr. 17, 2019, in Press)

Abstract PDF 

presented by Lim

April 15, 2019
Stability Effect of Quinary Interactions Reversed by Single Point Mutations

J. Am. Chem. Soc., 2019, 141 (11), pp 4660–4669

Abstract / PDF

presented by Nawrocki

March 25, 2019
Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

Kruse, H., Banas, P., & Šponer, J. (2018). Investigations of stacked DNA base-pair steps: highly accurate stacking interaction energies, energy decomposition, and many-body stacking effects. Journal of chemical theory and computation15(1), 95-115.

Abstract  PDF  SI

Presented by Maciej

 

February 18, 2019
Role of Conformational Flexibility in Monte Carlo Simulations of Many-Protein Systems

Majumdar, B. B., Prytkova, V., Wong, E. K., Freites, J. A., Tobias, D. J., and Heyden, M., JCTC (2019) 15 (2), 1399–1408

Abstract PDF 

presented by Lim

February 11, 2019
Promoter Distortion and Opening in the RNA Polymerase II Cleft

C. Dienemann, B Schwalb, S. Schilbach, and P. Cramer
Molecular Cell, 73, 97-106.e4, 2019

Abstract / PDF

presented by Bercem

February 4, 2019
Surface Charge Modulates Protein–Protein Interactions in Physiologically Relevant Environments

Biochemistry, 2018, 57 (11), 1681–1684

Abstract / PDF

presented by Nawrocki

January 28, 2019
Machine Learning of coarse-grained Molecular Dynamics Force Fields

Jiang Wang, Christoph Wehmeyer, Frank Noé, and Cecilia Clementi, Machine Learning of coarse-grained Molecular Dynamics Force Fields, arXiv (uploaded Dec. 08, 2018).

Abstract PDF 

presented by Lim