Journal club

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

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

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

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

August 27, 2018
The temperature dependence of the helical twist of DNA

 

Kriegel, Franziska, et al. "The temperature dependence of the helical twist of DNA." Nucleic acids research (2018).

 

Abstract / PDF

 

Presented by Maciej

August 13, 2018
Polymorphism of Lysozyme Condensates

M. S. Safari, M. C. Byington, J. C. Conrad, P. G. Vekilov

J. Phys. Chem. B, 2017, 121, pp 9091–9101

Abstract / PDF

presented by Nawrocki

August 13, 2018
DeepSite: protein-binding site predictor using 3D-convolutional neural networks

J. Jimenez, S. Doerr, G. Martinez-Rosell, A. S. Rose, G. De Fabritiis, Bioinformatics, 33(19), 2017, 3036-3042

PDF

Presented by Jaie

August 6, 2018
Improving low-accuracy protein structures using enhanced sampling techniques

Zhang, T., Ma, T., Wang, Q., and Ma, J., The Journal of Chemical Physics, 149, 072319 (2018).

PDF 

presented by Lim

July 30, 2018
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model

Spasic, Aleksandar, et al. "Improving RNA nearest neighbor parameters for helices by going beyond the two-state model." Nucleic acids research 46.10 (2018): 4883-4892.

PDF / Abstract

Presented by Maciej

July 9, 2018
Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations

Max Linke, Jurgen Kofinger, and Gerhard Hummer

J. Phys. Chem. B, 2018, 122 (21), pp 5630–5639

Abstract / PDF

presented by Nawrocki