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Protein structure databases

Identification of potential interleukin-8 inhibitors acting on the interactive site between chemokine and CXCR2 receptor: A computational approach

Thi-Thuy-Nga Tran, Que-Huong Tran, Quoc-Thai Nguyen, Minh-Tri Le, Dieu-Thuong Thi Trinh, Khac-Minh Thai

published 24 Feb 2022

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Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria

Elmira Nazarshodeh, Sayed-Amir Marashi, Sajjad Gharaghani

published 14 Dec 2021

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Principal component analysis of alpha-helix deformations in transmembrane proteins

Alexander Bevacqua, Sachit Bakshi, Yu Xia

published 15 Sep 2021

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PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

Bulat Faezov, Roland L. Dunbrack Jr.

published 06 Jul 2021

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Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach

Gwangho Lee, Gun Hyuk Jang, Ho Young Kang, Giltae Song

published 25 Jun 2021

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Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2’s pathogenicity factors

Ömür Baysal, Naeem Abdul Ghafoor, Ragıp Soner Silme, Alexander N. Ignatov, Volha Kniazeva

published 27 May 2021

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MCPdb: The bacterial microcompartment database

Jessica M. Ochoa, Kaylie Bair, Thomas Holton, Thomas A. Bobik, Todd O. Yeates

published 29 Mar 2021

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Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba

Logan Tillery, Kayleigh Barrett, Jenna Goldstein, Jared W. Lassner, Bram Osterhout, Nathan L. Tran, Lily Xu, Ryan M. Young, Justin Craig, Ian Chun, David M. Dranow, Jan Abendroth, Silvia L. Delker, Douglas R. Davies, Stephen J. Mayclin, Brandy Calhoun, Madison J. Bolejack, Bart Staker, Sandhya Subramanian, Isabelle Phan, Donald D. Lorimer, Peter J. Myler, Thomas E. Edwards, Dennis E. Kyle, Christopher A. Rice, James C. Morris, James W. Leahy, Roman Manetsch, Lynn K. Barrett, Craig L. Smith, Wesley C. Van Voorhis

published 24 Mar 2021

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A chemical interpretation of protein electron density maps in the worldwide protein data bank

Sen Yao, Hunter N. B. Moseley

published 12 Aug 2020

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A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy

Sheng-Hung Juan, Teng-Ruei Chen, Wei-Cheng Lo

published 30 Jun 2020

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Structure-based drug repositioning explains ibrutinib as VEGFR2 inhibitor

Melissa F. Adasme, Daniele Parisi, Kristien Van Belle, Sebastian Salentin, V. Joachim Haupt, Gary S. Jennings, Jörg-Christian Heinrich, Jean Herman, Ben Sprangers, Thierry Louat, Yves Moreau, Michael Schroeder

published 27 May 2020

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Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction

Maxim Shapovalov, Roland L. Dunbrack Jr., Slobodan Vucetic

published 06 May 2020

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QUATgo: Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding

Chi-Hua Tung, Ching-Hsuan Chien, Chi-Wei Chen, Lan-Ying Huang, Yu-Nan Liu, Yen-Wei Chu

published 29 Apr 2020

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