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Protein structure determination  
PLOS Computational Biology  
Exploring the potential of structure-based deep learning approaches for T cell receptor design

Helder V. Ribeiro-Filho, Gabriel E. Jara, João V. S. Guerra, Melyssa Cheung, Nathaniel R. Felbinger, José G. C. Pereira, Brian G. Pierce, Paulo S. Lopes-de-Oliveira

Research Article | published 30 Sep 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012489

Views: 1798Citations: 1Saves: 0 • Shares: 0

A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures

Noah B. Herrington, Yan Chak Li, David Stein, Gaurav Pandey, Avner Schlessinger

Research Article | published 24 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012302

Views: 2968Citations: 6Saves: 8 • Shares: 16

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2

R. Dustin Schaeffer, Jing Zhang, Kirill E. Medvedev, Lisa N. Kinch, Qian Cong, Nick V. Grishin

Research Article | published 28 Feb 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011586

Views: 1466Citations: 10Saves: 6 • Shares: 1

The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement

Arron Bale, Robert Rambo, Christopher Prior

Research Article | published 27 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011248

Views: 931Citations: 3Saves: 5 • Shares: 3

chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling

Maxx H. Tessmer, Stefan Stoll

Research Article | published 31 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010834

Views: 2116Citations: 31Saves: 16 • Shares: 2

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

Raphael R. Eguchi, Christian A. Choe, Po-Ssu Huang

Research Article | published 27 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010271

Views: 9303Citations: 85Saves: 68 • Shares: 2

Induced fit with replica exchange improves protein complex structure prediction

Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray

Research Article | published 03 Jun 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010124

Views: 3643Citations: 8Saves: 27 • Shares: 8

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Jon Kapla, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent, Jens Carlsson

Research Article | published 13 May 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008936

Views: 6093Citations: 24Saves: 68 • Shares: 13

Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins

Rahmatullah Roche, Sutanu Bhattacharya, Debswapna Bhattacharya

Research Article | published 23 Feb 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008753

Views: 2229Citations: 9Saves: 18 • Shares: 9

REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution

Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar

Research Article | published 01 Feb 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008060

Views: 2087Citations: 8Saves: 21 • Shares: 3

ProMod3—A versatile homology modelling toolbox

Gabriel Studer, Gerardo Tauriello, Stefan Bienert, Marco Biasini, Niklaus Johner, Torsten Schwede

Research Article | published 28 Jan 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008667

Views: 7075Citations: 216Saves: 216 • Shares: 6

The complexity of protein interactions unravelled from structural disorder

Beatriz Seoane, Alessandra Carbone

Research Article | published 08 Jan 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008546

Views: 3649Citations: 22Saves: 26 • Shares: 7

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein

Research Article | published 30 Nov 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008291

Views: 13077Citations: 109Saves: 137 • Shares: 8

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs

Brian Joseph Bender, Brennica Marlow, Jens Meiler

Research Article | published 28 Oct 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007597

Views: 5488Citations: 42Saves: 62 • Shares: 15

Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination

Yoonjoo Choi, Sukyo Jeong, Jung-Min Choi, Christian Ndong, Karl E. Griswold, Chris Bailey-Kellogg, Hak-Sung Kim

Research Article | published 31 Aug 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008150

Views: 3055Citations: 4Saves: 9 • Shares: 2

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