Journal club

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

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

July 9, 2018
Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field

K. Olesen, N. Awasthi, D. S. Bruhn, W. Pezeshkian and H. Khandelia
J. Chem. Theory Comput., 2018, 14, 3342-3350

Abstract / PDF

presented by Bercem

June 18, 2018
Developing a molecular dynamics force field for both folded and disordered protein states

Robustelli, P., Stefano, P., Shaw, D.E. (2018). Proceedings of the National Academy of Sciences, 115(21), E4758-66.

AbstractPDF

presented by Jaie

June 11, 2018
DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. - Copy

Qian, Z., Zhurkin, V. B., & Adhya, S. (2017). Proceedings of the National Academy of Sciences, 114(46), 12225-12230.

Abstract

PDF

presented by Maciej

June 11, 2018
Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

Narayanan, C. et al., Structure, 2018, 26 (3), p426-436.

PDF 

presented by Lim

May 7, 2018
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

N. Plattner, S. Doerr, G. De Fabritiis, and F. Noe

Nature Chemistry volume 9, pages 10051011 (2017)

Abstract / PDF

presented by Nawrocki

May 7, 2018
Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup–Solute Interactions

N. Pokhrel and L. Maibaum.
J. Chem. Theory Comput., 2018, 14, 1762-1771

Abstract / PDF

presented by Bercem

April 30, 2018
Protein homology model refinement by large-scale energy optimization

Park, H., Ovchinnikov, S., Kim, D. E., DiMaio, F., and Baker, D., Proc. Natl. Acad. Sci, USA, 2018, 115 (12) 3054-3059.

PDF 

presented by Lim

April 23, 2018
Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Lioy, Virginia S., et al. "Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins." Cell (2018).

PDF / abstract

Presented by Maciej

April 23, 2018
Highly Disordered Amyloid-beta Monomer Probed by Single-Molecule FRET and MD Simulation

F. Meng, M.M.J. Bellaiche, J-Y. Kim, G.H. Zerze, R. Best, H.S. Chung, Biophysical Journal, 2018, 114, 870-884

Abstract | PDF

presented by Jaie

March 26, 2018
Trigger loop of RNA polymerase is a positional, not acid–base, catalyst for both transcription and proofreading

T. V. Mishanina, M. Z. Palo, D. Nayak, R. A. Mooney and R. Landick.
PNAS, 2017, 114, .

Abstract / PDF

presented by Bercem

March 26, 2018
Peptide Solubility Limits: Backbone and Side-Chain Interactions

Rahul Sarma, Ka-Yiu Wong, Gillian C. Lynch, and B. Montgomery Pettitt

J. Phys. Chem. B 2018.

Abstract / PDF

presented by Nawrocki

March 5, 2018
RNA force field with accuracy comparable to state-of-the-art protein force fields

Tan, Dazhi, et al. "RNA force field with accuracy comparable to state-of-the-art protein force fields." Proceedings of the National Academy of Sciences(2018): 201713027.

PDF / abstract

Presented by Maciej

 

March 5, 2018
Rational design of proteins that exchange on functional timescales

Davey, J. A., Damry, A. M., Goto, N. K., and Chica, R. A., Nat. Chem. Biol., 2017, 13, 1280-1285.

Abstract / PDF 

presented by Lim

February 26, 2018
Development of a Coarse-Grained Model of Collagen-Like Peptide (CLP) for Studies of CLP Triple Helix Melting

J.E. Condon, A. Jayaraman, J. Phys. Chem. B, 2018, 122, 1929-1939

Abstract / PDF

presented by Jaie