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Protein structure databases  
PLOS Computational Biology  
Protein superfolds are characterised as frustration-free topologies: A case study of pure parallel β-sheet topologies

Hiroto Murata, Kazuma Toko, George Chikenji

Research Article | published 07 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012282

Views: 2118Citations: 1Saves: 0 • Shares: 0

DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models

Robby Concha-Eloko, Michiel Stock, Bernard De Baets, Yves Briers, Rafael Sanjuán, Pilar Domingo-Calap, Dimitri Boeckaerts

Software | published 05 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011831

Views: 1841Citations: 4Saves: 24 • Shares: 16

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

Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset

Simon K. S. Chu, Kush Narang, Justin B. Siegel

Research Article | published 22 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012248

Views: 1708Citations: 2Saves: 21 • Shares: 7

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco

Education | published 20 Jun 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012173

Views: 1069Citations: 0Saves: 7 • Shares: 0

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

Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Te Liu, Sichao Huang, Qian Zhang, Yu Xia, Manjie Zhang, Bin Sun

Research Article | published 07 Feb 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011519

Views: 853Citations: 0Saves: 0 • Shares: 0

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

Pathfinder: Protein folding pathway prediction based on conformational sampling

Zhaohong Huang, Xinyue Cui, Yuhao Xia, Kailong Zhao, Guijun Zhang

Research Article | published 11 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011438

Views: 2380Citations: 2Saves: 0 • Shares: 0

Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning

Li Xie, Lei Xie

Research Article | published 17 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010974

Views: 1580Citations: 6Saves: 25 • Shares: 1

Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes

Kevin Sawade, Andreas Marx, Christine Peter, Oleksandra Kukharenko

Research Article | published 01 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010531

Views: 1149Citations: 0Saves: 7 • Shares: 1

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

William Sheffler, Erin C. Yang, Quinton Dowling, Yang Hsia, Chelsea N. Fries, Jenna Stanislaw, Mark D. Langowski, Marisa Brandys, Zhe Li, Rebecca Skotheim, Andrew J. Borst, Alena Khmelinskaia, Neil P. King, David Baker

Research Article | published 22 May 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010680

Views: 3975Citations: 23Saves: 19 • Shares: 0

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Luis F. Garcia-Alles, Miguel Fuentes-Cabrera, Gilles Truan, David Reguera

Research Article | published 05 Apr 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011038

Views: 1158Citations: 6Saves: 6 • Shares: 1

Dissecting peripheral protein-membrane interfaces

Thibault Tubiana, Ian Sillitoe, Christine Orengo, Nathalie Reuter

Research Article | published 14 Dec 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010346

Views: 2253Citations: 18Saves: 25 • Shares: 16

Soft disorder modulates the assembly path of protein complexes

Beatriz Seoane, Alessandra Carbone

Research Article | published 17 Nov 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010713

Views: 1851Citations: 8Saves: 10 • Shares: 8

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