Journal club

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

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 biology, 19(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
David Gnutt, Stepan Timr, Jonas Ahlers, Benedikt König, Emily Manderfeld, Matthias Heyden, Fabio Sterpone, and Simon Ebbinghaus
 

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 computation, 15(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
Alex J. Guseman, Shannon L. Speer, Gerardo M. Perez Goncalves and Gary J. Pielak
 

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

January 21, 2019
Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.

Templeton, Clark, and Ron Elber. "Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix–Junction–Helix Systems." Journal of the American Chemical Society 140.49 (2018): 16948-16951.

Abstract 

PDF

presented by Maciej

January 14, 2019
Liquid-Liquid Phase Separation of Patchy Particles Illuminates Diverse Effects of Regulatory Components on Protein Droplet Formation

V. Nguemaha and H.-X. Zhou
Scientific Reports, 8:6728, 2018

Abstract

presented by Bercem

January 7, 2019
Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions
Philipp Honegger, Michael Schmollngruber and Othmar Steinhauser
 

Phys. Chem. Chem. Phys., 2018,20, 19581-19594

Abstract / PDF

presented by Nawrocki

December 10, 2018
RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

B. Treeck, D. S. W. Protter, T. Matheny, A. Khong, C. D. Link, and R. Parker
PNAS, 115, 2734-2739,2018

Abstract / PDF

presented by Bercem

December 10, 2018
Distance-based Protein Folding powered by Deep Learning

Jinbo Xu, Distance-based Protein Folding powered by Deep Learning, bioXriv (uploaded Nov. 11, 2018).

Abstract PDF 

presented by Lim

November 26, 2018
End-to-End'stacking of small dsRNA

Erlenbach, N., Grünewald, C., Krstic, B., Heckel, A., & Prisner, T. F. (2018). ‘End-to-End’stacking of small dsRNA. RNA, rna-068130.

PDF / Abstract 

Figures

November 19, 2018
Discovering a Transferable Charge Assignment Model Using Machine Learning

A.E. Sifain, N. Lubbers, B.T. Nebgen, J.S. Smith, A.Y. Lokhov, O. Isayev, A.E. Roitberg, K. Barros, S. Tretiak

Journal of Physical Chemistry Letters, 2018, 9, 4495-4501

PDF

Presented by Jaie

November 12, 2018
Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

Z. Bashardanesh and D. van der Spoel

J. Phys. Chem. B, 2018, 122 (33), pp 8018–8027

Abstract / PDF

presented by Nawrocki

October 1, 2018
RNA polymerase II clustering through carboxy-terminal domain phase separation

M. Boehning, C. Dugast-Darzacq, M. Rankovic, A. S. Hansen, T. Yu,.H. Marie-Nelly, D. T. McSwiggen, G. Kokic, G. M. Dailey, P. Cramer*, X. Darzacq* and M. Zweckstetter
Nature Structural & Molecular Biology, 25, 833-840, 2018

Abstract / PDF

presented by Bercem

October 1, 2018
Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

Wehmeyer, C. and Noé, F., The Journal of Chemical Physics, 148, 241703 (2018). 

PDF 

presented by Lim