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Protein structure determination  
PLOS One  
Navigating the unstructured by evaluating alphafold’s efficacy in predicting missing residues and structural disorder in proteins

Sen Zheng

Research Article | published 25 Mar 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0313812

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Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction

Neshatul Haque, Jessica B. Wagenknecht, Brian D. Ratnasinghe, Michael T. Zimmermann

Research Article | published 26 Nov 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0313308

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GTExome: Modeling commonly expressed missense mutations in the human genome

Jill Hoffman, Henry Tan, Clara Sandoval-Cooper, Kaelyn de Villiers, Scott M. Reed

Research Article | published 30 May 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0303604

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Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F

Alper Karagöl, Taner Karagöl, Eva Smorodina, Shuguang Zhang

Research Article | published 10 Apr 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0289644

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Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Derek L. Bolhuis, Ram Dixit, Kevin C. Slep

Research Article | published 29 Dec 2023 PLOS ONE

https://doi.org/10.1371/journal.pone.0290024

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Computational analysis of the functional and structural impact of the most deleterious missense mutations in the human Protein C

Mahvash Farajzadeh-Dehkordi, Ladan Mafakher, Abbas Harifi, Fatemeh Samiee-Rad, Babak Rahmani

Research Article | published 28 Nov 2023 PLOS ONE

https://doi.org/10.1371/journal.pone.0294417

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Crystallographic structure determination and analysis of a potential short-chain dehydrogenase/reductase (SDR) from multi-drug resistant Acinetobacter baumannii

Seyed Mohammad Ghafoori, Soha Abdollahpour, Paniz Shirmast, Jade K. Forwood

Research Article | published 24 Aug 2023 PLOS ONE

https://doi.org/10.1371/journal.pone.0289992

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The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction

Bejo Ropii, Maulidwina Bethasari, Isa Anshori, Allya Paramita Koesoema, Wervyan Shalannanda, Ardianto Satriawan, Casi Setianingsih, Mohammad Rizki Akbar, Reza Aditama

Research Article | published 27 Jul 2023 PLOS ONE

https://doi.org/10.1371/journal.pone.0288684

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CryoEM structure and Alphafold molecular modelling of a novel molluscan hemocyanin

Gaia Pasqualetto, Andrew Mack, Emily Lewis, Ryan Cooper, Alistair Holland, Ufuk Borucu, Judith Mantell, Tom Davies, Miriam Weckener, Dan Clare, Tom Green, Pete Kille, Alex Muhlhozl, Mark T. Young

Research Article | published 22 Jun 2023 PLOS ONE

https://doi.org/10.1371/journal.pone.0287294

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Emulation of the structure of the Saposin protein fold by a lung surfactant peptide construct of surfactant Protein B

Alan J. Waring, Julian P. Whitelegge, Shantanu K. Sharma, Larry M. Gordon, Frans J. Walther

Research Article | published 03 Nov 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0276787

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Structure of Klebsiella pneumoniae adenosine monophosphate nucleosidase

Brian C. Richardson, Roger Shek, Wesley C. Van Voorhis, Jarrod B. French

Research Article | published 20 Oct 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0275023

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In silico functional annotation of hypothetical proteins from the Bacillus paralicheniformis strain Bac84 reveals proteins with biotechnological potentials and adaptational functions to extreme environments

Md. Atikur Rahman, Uzma Habiba Heme, Md. Anowar Khasru Parvez

Research Article | published 13 Oct 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0276085

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New insights into disordered proteins and regions according to the FOD-M model

Irena Roterman, Katarzyna Stapor, Piotr Fabian, Leszek Konieczny

Research Article | published 10 Oct 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0275300

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Validation of the solution structure of dimerization domain of PRC1

Fei Tan, Jin Xu

Research Article | published 05 Aug 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0270572

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AlphaFold2 and RoseTTAFold predict posttranslational modifications. Chromophore formation in GFP-like proteins

Sophia M. Hartley, Kelly A. Tiernan, Gjina Ahmetaj, Adriana Cretu, Yan Zhuang, Marc Zimmer

Research Article | published 16 Jun 2022 PLOS ONE

https://doi.org/10.1371/journal.pone.0267560

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