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PLOS Computational Biology  
Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts

Ikram Mahmoudi, Chloé Quignot, Carla Martins, Jessica Andreani

Research Article | published 03 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012650

Views: 829Citations: 0Saves: 0 • Shares: 0

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

Samuel E. Hoff, F. Emil Thomasen, Kresten Lindorff-Larsen, Massimiliano Bonomi

Research Article | published 15 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012180

Views: 1417Citations: 5Saves: 0 • Shares: 0

Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7

Akseli Niemelä, Artturi Koivuniemi

Research Article | published 28 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012137

Views: 633Citations: 0Saves: 0 • Shares: 0

Programming co-assembled peptide nanofiber morphology via anionic amino acid type: Insights from molecular dynamics simulations

Xin Y. Dong, Renjie Liu, Dillon T. Seroski, Gregory A. Hudalla, Carol K. Hall

Research Article | published 04 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011685

Views: 1201Citations: 2Saves: 0 • Shares: 0

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase

Gabriel Monteiro da Silva, Jordan Yang, Bunlong Leang, Jessie Huang, Daniel M. Weinreich, Brenda M. Rubenstein

Research Article | published 27 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009944

Views: 3523Citations: 0Saves: 14 • Shares: 4

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

Francesco Trozzi, Feng Wang, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao

Research Article | published 26 Jul 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009168

Views: 2211Citations: 4Saves: 19 • Shares: 1

Evaluation of residue-residue contact prediction methods: From retrospective to prospective

Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo, Yanjie Wei

Research Article | published 24 May 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009027

Views: 4035Citations: 24Saves: 32 • Shares: 3

How multisite phosphorylation impacts the conformations of intrinsically disordered proteins

Fan Jin, Frauke Gräter

Research Article | published 04 May 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008939

Views: 5501Citations: 50Saves: 53 • Shares: 6

Insights on cross-species transmission of SARS-CoV-2 from structural modeling

João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt

Research Article | published 03 Dec 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008449

Views: 8358Citations: 58Saves: 148 • Shares: 61

Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain

Vikas Dubey, Behruz Bozorg, Daniel Wüstner, Himanshu Khandelia

Research Article | published 06 Oct 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007554

Views: 3425Citations: 15Saves: 23 • Shares: 9

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Bogdan Barz, Jennifer Loschwitz, Birgit Strodel

Research Article | published 07 Oct 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007193

Views: 4767Citations: 19Saves: 23 • Shares: 5

Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies

Monica Civera, Francesca Vasile, Donatella Potenza, Cinzia Colombo, Sara Parente, Chiara Vettraino, Tommaso Prosdocimi, Emilio Parisini, Laura Belvisi

Research Article | published 03 Jun 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007041

Views: 2730Citations: 6Saves: 10 • Shares: 4

Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase

Daniel S. Moore, Conor Brines, Heather Jewhurst, John P. Dalton, Irina G. Tikhonova

Research Article | published 31 Oct 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006525

Views: 5494Citations: 11Saves: 19 • Shares: 1

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)

Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang

Research Article | published 26 Oct 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006511

Views: 4234Citations: 30Saves: 28 • Shares: 3

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

Tatu Pantsar, Sami Rissanen, Daniel Dauch, Tuomo Laitinen, Ilpo Vattulainen, Antti Poso

Research Article | published 10 Sep 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006458

Views: 11667Citations: 68Saves: 121 • Shares: 5

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