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Large scale paired antibody language models

Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane

Research Article | published 06 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012646

Views: 1370Citations: 3Saves: 0 • Shares: 0

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

Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation

Marc D. Singleton, Michael B. Eisen

Research Article | published 25 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012028

Views: 2089Citations: 4Saves: 0 • Shares: 0

A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution

Patrick Gemmell, Timothy B. Sackton, Scott V. Edwards, Jun S. Liu

Research Article | published 24 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011995

Views: 1407Citations: 3Saves: 0 • Shares: 0

Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment

Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard

Research Article | published 17 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011621

Views: 1380Citations: 5Saves: 0 • Shares: 0

Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution

Joeri van Strien, Felix Evers, Madhurya Lutikurti, Stijn L. Berendsen, Alejandro Garanto, Geert-Jan van Gemert, Alfredo Cabrera-Orefice, Richard J. Rodenburg, Ulrich Brandt, Taco W. A. Kooij, Martijn A. Huynen

Research Article | published 07 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011090

Views: 900Citations: 1Saves: 0 • Shares: 0

RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure

Elena Rivas

Research Article | published 14 Jul 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011262

Views: 1393Citations: 5Saves: 0 • Shares: 0

Pleiotropy promotes the evolution of inducible immune responses in a model of host-pathogen coevolution

Reese A. Martin, Ann T. Tate

Research Article | published 06 Apr 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010445

Views: 1254Citations: 3Saves: 10 • Shares: 13

Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates

Christoffer Norn, Ingemar André

Research Article | published 24 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010262

Views: 1212Citations: 4Saves: 0 • Shares: 0

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers

Sean B. King, Mona Singh

Research Article | published 23 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010966

Views: 1084Citations: 0Saves: 0 • Shares: 0

Inferring protein fitness landscapes from laboratory evolution experiments

Sameer D’Costa, Emily C. Hinds, Chase R. Freschlin, Hyebin Song, Philip A. Romero

Research Article | published 01 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010956

Views: 3329Citations: 12Saves: 0 • Shares: 0

Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution

Rikuto Kamiura, Ryo Mizuuchi, Norikazu Ichihashi

Research Article | published 01 Dec 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010709

Views: 1855Citations: 3Saves: 9 • Shares: 10

Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes

Leonardo Trujillo, Paul Banse, Guillaume Beslon

Research Article | published 31 Oct 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010647

Views: 1803Citations: 2Saves: 7 • Shares: 4

DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets

Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio

Research Article | published 19 Oct 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010610

Views: 2105Citations: 7Saves: 5 • Shares: 12

Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases?

Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Tomasz Skalski, Aleksandra Samol, Weronika Bagrowska, Tomasz Magdziarz, Artur Góra

Research Article | published 17 May 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010119

Views: 2509Citations: 8Saves: 17 • Shares: 11

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