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Protein structure databases  
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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The binding modes of brazilin and hematein from Caesalpinia sappan L. to Cutibacterium acnes lipase: Simulation studies

Maneenuch Pengsawang, Borvornwat Toviwek, Winyoo Sangthong, Apaporn Boonmee, Phoom Chairatana, Prapasiri Pongprayoon

Research Article | published 04 Mar 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0318706

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Drug target affinity prediction based on multi-scale gated power graph and multi-head linear attention mechanism

Shuo Hu, Jing Hu, Xiaolong Zhang, Shuting Jin, Xin Xu

Research Article | published 21 Feb 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0315718

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Investigation of biometabolites and novel antimicrobial peptides derived from promising source Cordyceps militaris and effect of non-small cell lung cancer genes computationally

Muhammad Afzal, Mai Abdel Haleem A. Abusalah, Neelum Shehzadi, Muhammad Absar, Naveed Ahmed, Sarmir Khan, Yalnaz Naseem, Noshaba Mehmood, Kirnpal Kaur Banga Singh

Research Article | published 23 Jan 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0310103

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Ongoing measles outbreak in Romania: Clinical investigation and molecular epidemiology performed on whole genome sequences

Robert Hohan, Marius Surleac, Victor Daniel Miron, Andreea Tudor, Ana-Maria Tudor, Oana Săndulescu, Ovidiu Vlaicu, Victoria Aramă, Daniela Pițigoi, Adriana Hristea, Anca Cristina Drăgănescu, Dimitrios Paraskevis, Leontina Bănică, Dan Oțelea, Simona Paraschiv

Research Article | published 15 Jan 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0317045

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Fracture-healing effects of Rhizoma Musae ethanolic extract: An integrated study using UHPLC-Q-Exactive-MS/MS, network pharmacology, and molecular docking

Jian Zhang, Wanyan Shen, Fanzhi Liu, Hehe He, Shuquan Han, Lina Luo

Research Article | published 14 Jan 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0313743

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Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Ranjit K. Deka, Shih-Chia Tso, Wei Z. Liu, Chad A. Brautigam

Research Article | published 09 Jan 2025 PLOS ONE

https://doi.org/10.1371/journal.pone.0312642

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Integration of pharmacophore-based virtual screening, molecular docking, ADMET analysis, and MD simulation for targeting EGFR: A comprehensive drug discovery study using commercial databases

Abdullah R. Alanzi, Ashaimaa Y. Moussa, Mohammed S. Alsalhi, Tayyab Nawaz, Ijaz Ali

Research Article | published 09 Dec 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0311527

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Computational investigation of naturally occurring anticancer agents in regulating Hedgehog pathway proteins

Renu Pai, Divijendranatha Reddy Sirigiri, Rajyalakshmi Malempati, Saisha Vinjamuri

Research Article | published 03 Dec 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0311307

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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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Ononin delays the development of osteoarthritis by down-regulating MAPK and NF-κB pathways in rat models

Fang Xu, Zhaocong Li, Yueming Jiang, Ting Liao, Michael Aschner, Qingjun Wei

Research Article | published 31 Oct 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0310293

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Assessing anti oxidant, antidiabetic potential and GCMS profiling of ethanolic root bark extract of Zanthoxylum rhetsa (Roxb.) DC: Supported by in vitro, in vivo and in silico molecular modeling

Apurba Kumar Barman, Sumaiya Mahadi, Md Arju Hossain, Rahima Begum, Rabindra Nath Acharyya, Marjana Alam, Md. Habibur Rahman, Nripendra Nath Biswas, A. S. M. Monjur Al Hossain

Research Article | published 19 Aug 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0304521

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An in silico investigation on the binding site preference of PD-1 and PD-L1 for designing antibodies for targeted cancer therapy

Sarah Abdolmaleki, Mazdak Ganjalikhani hakemi, Mohamad Reza Ganjalikhany

Research Article | published 25 Jul 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0304270

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Bioinformatics for Dentistry: A secondary database for the genetics of tooth development

Ava K. Chow, Rachel Low, Jerald Yuan, Karen K. Yee, Jaskaranjit Kaur Dhaliwal, Shanice Govia, Nazlee Sharmin

Research Article | published 06 Jun 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0303628

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Atomistic description of the OCTN1 recognition mechanism via in silico methods

Omar Ben Mariem, Luca Palazzolo, Beatrice Torre, Yao Wei, Davide Bianchi, Uliano Guerrini, Tommaso Laurenzi, Simona Saporiti, Emma De Fabiani, Lorena Pochini, Cesare Indiveri, Ivano Eberini

Research Article | published 03 Jun 2024 PLOS ONE

https://doi.org/10.1371/journal.pone.0304512

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