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PLOS Computational Biology  
Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds

Fei Cai, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, Yingnan Zhang

Research Article | published 18 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012609

Views: 751Citations: 1Saves: 4 • Shares: 2

Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins

Javier A. Romero, Paulina Putko, Mateusz Urbańczyk, Krzysztof Kazimierczuk, Anna Zawadzka-Kazimierczuk

Research Article | published 06 Oct 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010258

Views: 1651Citations: 5Saves: 19 • Shares: 7

SPEACH_AF: Sampling protein ensembles and conformational heterogeneity with Alphafold2

Richard A. Stein, Hassane S. Mchaourab

Research Article | published 22 Aug 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010483

Views: 7917Citations: 146Saves: 83 • Shares: 14

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

From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

Ana Zafra Ruano, Elisa Cilia, José R. Couceiro, Javier Ruiz Sanz, Joost Schymkowitz, Frederic Rousseau, Irene Luque, Tom Lenaerts

Research Article | published 23 May 2016 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1004938

Views: 2475Citations: 5Saves: 33 • Shares: 1

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

Claire Colas, Christof Grewer, Nicholas James Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger

Research Article | published 07 Oct 2015 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1004477

Views: 7662Citations: 65Saves: 76 • Shares: 4

Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces

Cahit Dalgicdir, Christoph Globisch, Christine Peter, Mehmet Sayar

Research Article | published 21 Aug 2015 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1004328

Views: 6438Citations: 36Saves: 45 • Shares: 2

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors

Lars Boukharta, Hugo Gutiérrez-de-Terán, Johan Åqvist

Research Article | published 17 Apr 2014 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1003585

Views: 10240Citations: 63Saves: 91 • Shares: 3

Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization

Rudi Agius, Mieczyslaw Torchala, Iain H. Moal, Juan Fernández-Recio, Paul A. Bates

Research Article | published 05 Sep 2013 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1003216

Views: 6732Citations: 31Saves: 0 • Shares: 0

Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e

Elisa Cilia, Geerten W. Vuister, Tom Lenaerts

Research Article | published 29 Nov 2012 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1002794

Views: 3938Citations: 26Saves: 0 • Shares: 0

Structural Consensus among Antibodies Defines the Antigen Binding Site

Vered Kunik, Bjoern Peters, Yanay Ofran

Research Article | published 23 Feb 2012 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1002388

Views: 13122Citations: 110Saves: 204 • Shares: 0

Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity

Daniel J. Cole, Eeson Rajendra, Meredith Roberts-Thomson, Bryn Hardwick, Grahame J. McKenzie, Mike C. Payne, Ashok R. Venkitaraman, Chris-Kriton Skylaris

Research Article | published 14 Jul 2011 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1002096

Views: 6877Citations: 36Saves: 0 • Shares: 0

Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach

Khyati Kapoor, Mohd Rehan, Ajeeta Kaushiki, Ritu Pasrija, Andrew M. Lynn, Rajendra Prasad

Research Article | published 24 Dec 2009 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1000624

Views: 5617Citations: 24Saves: 0 • Shares: 0

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo

Research Article | published 26 Jun 2009 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1000415

Views: 13524Citations: 124Saves: 189 • Shares: 1

Protein–Protein Interaction Hotspots Carved into Sequences

Yanay Ofran, Burkhard Rost

Research Article | published 13 Jul 2007 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.0030119

Views: 33664Citations: 232Saves: 279 • Shares: 0

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