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Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases

JOURNAL ARTICLE published 14 February 2022 in Journal of Chemical Information and Modeling

Authors: Cecilia Chávez-García | Mikko Karttunen

https://doi.org/10.1021/acs.jcim.1c01501 Actions

Method To Assess Packing Quality of Transmembrane α-Helices in Proteins. 1. Parametrization Using Structural Data

JOURNAL ARTICLE published 1 May 2007 in Journal of Chemical Information and Modeling

Authors: Anton O. Chugunov | Valery N. Novoseletsky | Dmitry E. Nolde | Alexander S. Arseniev | Roman G. Efremov

https://doi.org/10.1021/ci600516x Actions

Exploration of Enzyme−Ligand Interactions in CYP2D6 & 3A4 Homology Models and Crystal Structures Using a Novel Computational Approach

JOURNAL ARTICLE published 1 May 2007 in Journal of Chemical Information and Modeling

Authors: Britta Kjellander | Collen M. Masimirembwa | Ismael Zamora

https://doi.org/10.1021/ci600561v Actions

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size

JOURNAL ARTICLE published 26 October 2009 in Journal of Chemical Information and Modeling

Authors: Axel Griewel | Ole Kayser | Jochen Schlosser | Matthias Rarey

https://doi.org/10.1021/ci9002415 Actions

MolTaut: A Tool for the Rapid Generation of Favorable Tautomer in Aqueous Solution

JOURNAL ARTICLE published 10 April 2023 in Journal of Chemical Information and Modeling

Research funded by National Natural Science Foundation of China (21933010)

Authors: Xiaolin Pan | Fanyu Zhao | Yueqing Zhang | Xingyu Wang | Xudong Xiao | John Z. H. Zhang | Changge Ji

https://doi.org/10.1021/acs.jcim.2c01393 Actions

Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Authors: Luke Landry | Pengfei Li

https://doi.org/10.1021/acs.jcim.3c01815 Actions

D3Rings: A Fast and Accurate Method for Ring System Identification and Deep Generation of Drug-Like Cyclic Compounds

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Research funded by National Key Research and Development Program of China (2022YFA1004304) | National Natural Science Foundation of China (82322067,82273851)

Authors: Minfei Ma | Xinben Zhang | Liping Zhou | Zijian Han | Yulong Shi | Jintian Li | Leyun Wu | Zhijian Xu | Weiliang Zhu

https://doi.org/10.1021/acs.jcim.3c01657 Actions

Predicting Protein–Protein Interactions Using Symmetric Logistic Matrix Factorization

JOURNAL ARTICLE published 26 April 2021 in Journal of Chemical Information and Modeling

Research funded by National Institute of General Medical Sciences (P41 GM103712)

Authors: Fen Pei | Qingya Shi | Haotian Zhang | Ivet Bahar

https://doi.org/10.1021/acs.jcim.1c00173 Actions

Characterization of Hydrophilic α-Helical Hot Spots on the Protein–Protein Interaction Interfaces for the Design of α-Helix Mimetics

JOURNAL ARTICLE published 25 April 2022 in Journal of Chemical Information and Modeling

Research funded by National Cancer Institute (P30-CA76292)

Authors: Zhen Wang | Haitao Ji

https://doi.org/10.1021/acs.jcim.1c01556 Actions

Issue Editorial Masthead

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

https://doi.org/10.1021/civ064i003_1768946 Actions

PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Research funded by Ministerio de Ciencia e Innovaci?n (PID2020-116564GB-I00,PTQ2021-011670) | H2020 Research Infrastructures (823712)

Authors: Mariona Torrens-Fontanals | Panagiotis Tourlas | Stefan Doerr | Gianni De Fabritiis

https://doi.org/10.1021/acs.jcim.3c01776 Actions

A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic Behavior of the Catalytic Site of the Tryptophan Synthase

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Authors: Anupom Roy | Mikko Karttunen

https://doi.org/10.1021/acs.jcim.3c01966 Actions

Variability of the DNA Backbone Geometry in DNA–Protein Complexes: Experimental Data Analysis

JOURNAL ARTICLE published 27 September 2021 in Journal of Chemical Information and Modeling

Research funded by Russian Academy of Sciences (0082-2019-0005)

Authors: Ivan A. Strelnikov | Natalya A. Kovaleva | Elena A. Zubova

https://doi.org/10.1021/acs.jcim.1c00506 Actions

Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Research funded by Natural Science Foundation of Hebei Province (B2021109004) | Dezhou University (2019xjrc335,2019xjrc334,2019xgrc46,2019xjrc336,2019xjrc333) | Natural Science Foundation of Shandong Province (ZR2021MB107) | National Natural Science Foundation of China (32171249)

Authors: Mingqiong Tong | Peng Liu | Chaoqun Li | Zhongyu Zhang | Wan Sun | Pingxuan Dong | Na Fan | Xiaoyue Wang | Jing Liu | Chao Lv | Zanxia Cao | Yan Wang

https://doi.org/10.1021/acs.jcim.3c01584 Actions

Structure Comparison of Beta Amyloid Peptide Aβ 1–42 Isoforms. Molecular Dynamics Modeling

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Research funded by Russian Science Foundation (19-74-30007)

Authors: Anna P. Tolstova | Alexander A. Makarov | Alexei A. Adzhubei

https://doi.org/10.1021/acs.jcim.3c01624 Actions

Cation–π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study

JOURNAL ARTICLE published 12 February 2024 in Journal of Chemical Information and Modeling

Research funded by Natural Science Foundation of Guangdong Province (2021A1515010068) | College Students' Innovation Training Program of Sun Yat-sen University (202210440)

Authors: Yunhao Mei | Yong Shen

https://doi.org/10.1021/acs.jcim.3c01883 Actions

Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions

JOURNAL ARTICLE published 1 November 2007 in Journal of Chemical Information and Modeling

Authors: Benjamin Breu | Katrin Silber | Holger Gohlke

https://doi.org/10.1021/ci7002472 Actions

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site

JOURNAL ARTICLE published 22 November 2021 in Journal of Chemical Information and Modeling

Research funded by National Institutes of Health (GM126140,GM138472)

Authors: Hugo Guterres | Sang-Jun Park | Yiwei Cao | Wonpil Im

https://doi.org/10.1021/acs.jcim.1c01156 Actions

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis

JOURNAL ARTICLE published 28 August 2023 in Journal of Chemical Information and Modeling

Research funded by Postdoctoral Research Foundation of China (2020M683144,2020TQ0390) | Special Project for Research and Development in Key areas of Guangdong Province (2022B1111080005) | National Natural Science Foundation of China (21773313,22103098)

Authors: Fan Zhang | Tao Zeng | Ruibo Wu

https://doi.org/10.1021/acs.jcim.3c00779 Actions

Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms

JOURNAL ARTICLE published 23 January 2023 in Journal of Chemical Information and Modeling

Research funded by Russian Science Foundation (21-74-20113)

Authors: Alexander Zlobin | Julia Belyaeva | Andrey Golovin

https://doi.org/10.1021/acs.jcim.2c01071 Actions
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