Article
Biochemical Research Methods
Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang
Summary: In this study, the protein-ligand interactions in monomeric and quaternary structures were compared using molecular docking experiments and binding free energy estimations. The results showed that ligands in quaternary structures can simultaneously interact with multiple protein chains, and quaternary structures have lower binding free energy and more accurate ligand conformations compared to monomeric structures. Therefore, it is recommended to use quaternary structures in future studies on protein-ligand interactions.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Palina Pliushcheuskaya, Georg Kuenze
Summary: Ion channels are involved in various essential biological processes and targeting them with drugs has potential therapeutic applications. However, the development of selective drugs for ion channels lags behind due to limited understanding. Computational approaches, especially structure-based drug design, can accelerate early stages of drug discovery and offer new opportunities for research. This review emphasizes the importance of integrating structural data, modeling, and chemoinformatics to identify and characterize new molecules targeting ion channels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Physics, Applied
Connor J. Morris, Dennis Della Corte
Summary: Molecular docking and molecular dynamics are powerful tools for studying protein-ligand interactions, predicting binding poses, affinities, and stability. They are widely used in drug discovery and further research on combining common molecular docking and MD methods is recommended for enhanced results.
MODERN PHYSICS LETTERS B
(2021)
Article
Biochemical Research Methods
Qilong Wu, Sheng-You Huang
Summary: Covalent inhibitors have attracted attention for their long residence time, high binding efficiency, and strong selectivity. The development of computational tools like HCovDock, an efficient docking algorithm for covalent protein-ligand interactions, is valuable for modeling and screening of covalent drugs. HCovDock outperforms seven other state-of-the-art covalent docking programs and exhibits a high success rate in reproducing experimentally observed structures and virtual screening.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Qilong Wu, Sheng-You Huang
Summary: Covalent inhibitors are highly valued for their long residence time, high binding efficiency, and strong selectivity. The development of computational tools like molecular docking, such as HCovDock, is important for modeling covalent protein-ligand interactions and screening potential drugs. HCovDock shows better performance than other state-of-the-art docking programs and has high success rates in reproducing experimentally observed structures.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Xiaocong Yang, Yang Liu, Jianhong Gan, Zhi-Xiong Xiao, Yang Cao
Summary: Protein-ligand docking is crucial in drug design and bioinformatics. FitDock, a new method, has shown significant improvement in docking success rate and speed compared to popular methods, especially when template structures are available.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sumin Lee, Seeun Kim, Gyu Rie Lee, Sohee Kwon, Hyeonuk Woo, Chaok Seok, Hahnbeom Park
Summary: This study explores the improvement in modeling and docking strategies for GPCR drug discovery through deep learning (DL) based protein structure predictions. It shows that substantial improvements have been achieved by correct functional-state modeling of receptors and receptor-flexible docking. The success rate of docking on DL-based model structures approaches that of cross-docking on experimental structures, showing over 30% improvement from previous pre-DL protocols. Best-practice modeling strategies and model confidence estimation metric proposed in this work can serve as a guideline for future computer-aided GPCR drug discovery scenarios.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemical Research Methods
Lianming Du, Chaoyue Geng, Qianglin Zeng, Ting Huang, Jie Tang, Yiwen Chu, Kelei Zhao
Summary: Molecular docking is a crucial approach in drug discovery and pharmaceutical research, and Dockey is a flexible and intuitive graphical interface tool that automates docking and analysis of large-scale ligands and receptors in parallel.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Seho Lee, Chaok Seok, Hahnbeom Park
Summary: In this study, we evaluate the usefulness of cryo-EM protein structures for in silico drug design by analyzing ligand docking accuracy. Our results show that medium resolution cryo-EM structures have lower docking success rates compared to high-resolution crystal structures. We identify the heterogeneity in protein conformations as the main factor causing docking difficulties in cryo-EM structures. We suggest the need for more robust method developments to fully utilize cryo-EM structures in drug design.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Murtala A. Ejalonibu, Segun A. Ogundare, Ahmed A. Elrashedy, Morufat A. Ejalonibu, Monsurat M. Lawal, Ndumiso N. Mhlongo, Hezekiel M. Kumalo
Summary: Developing new antibiotics targeting resistant Mycobacterium tuberculosis is an appealing strategy to combat the global tuberculosis epidemic, with computational techniques playing a key role in drug design and discovery. Recent advancements in technology have enhanced the chances of drug development, offering hope in the fight against tuberculosis resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Hugo Guterres, Sang-Jun Park, Han Zhang, Thomas Perone, Jongtaek Kim, Wonpil Im
Summary: Molecular docking is a popular computational tool in drug design, but has room for improvement. Molecular dynamics (MD) simulations of protein-ligand structures can enhance docking accuracy, and the CHARMM-GUI high-throughput simulator (HTS) is a tool for preparing MD simulation systems.
Article
Biochemistry & Molecular Biology
Jacopo Carbone, Alessia Ghidini, Antonio Romano, Luca Gentilucci, Francesco Musiani
Summary: PacDOCK is a free and user-friendly web server that helps analyze molecular docking results and improve the efficiency of computer-aided drug design.
Article
Chemistry, Physical
Parnashabari Sarkar, Saurabh Gupta, A. H. Udaya Kumar, Dipankar Das, Sourav Sutradhar, Kamaldeep Paul, N. K. Lokanath, Biswa Nath Ghosh
Summary: A one-pot method was utilized to prepare zinc and copper complexes of 4-methoxyphenyl-2,6-di(pyrazine-2-yl)pyridine ligand (L) for their potential as selective binders with serum albumins. The mononuclear complexes [CuL2]Cl2 (1) and [ZnL2]Cl2 (2) were obtained through the reaction of metal chlorides with ligand L. Characterization of the complexes was performed using various techniques, and their interactions with Human Serum Albumin (HSA) and drug displacement properties were investigated. Complex 1 showed higher binding capability towards HSA than complex 2, and both complexes exhibited better binding affinity than the free ligand. The fluorescence quenching of HSA by the complexes was found to be static in nature, and the binding constants were determined using the Stern-Volmer equation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Sohee Kwon, Chaok Seok
Summary: Protein-ligand docking is a crucial computational technique used for understanding protein functions and designing new molecules. One challenge in protein-ligand docking is accounting for protein conformational changes induced by ligand binding. This study introduces a docking method called CSAlign-Dock, which incorporates structure alignment to known complex structures and demonstrates superior performance.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Gabriele La Monica, Antonino Lauria, Alessia Bono, Annamaria Martorana
Summary: The approval of HIV-1 protease inhibitors marked an important step in AIDS treatment, but also led to severe side effects. In-silico techniques can help design new selective inhibitors with well-fitting selectivity and without undesirable interactions. This new method could be a reliable tool in the research of targeted small molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Chengfei Yan, Sam Z. Grinter, Benjamin Ryan Merideth, Zhiwei Ma, Xiaoqin Zou
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2016)
Article
Biochemistry & Molecular Biology
Xianjin Xu, Liming Qiu, Chengfei Yan, Zhiwei Ma, Sam Z. Grinter, Xiaoqin Zou
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2017)
Meeting Abstract
Biophysics
Sam Z. Grinter, Xiaoqin Zou
BIOPHYSICAL JOURNAL
(2012)
Article
Chemistry, Medicinal
Sam Z. Grinter, Chengfei Yan, Sheng-You Huang, Lin Jiang, Xiaoqin Zou
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2013)
Article
Chemistry, Multidisciplinary
Sam Z. Grinter, Xiaoqin Zou
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2014)
Article
Biochemical Research Methods
Sam Z. Grinter, Yayun Liang, Sheng-You Huang, Salman M. Hyder, Xiaoqin Zou
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2011)
Article
Chemistry, Physical
Hao-Yang Liu, Sam Z. Grinter, Xiaoqin Zou
JOURNAL OF PHYSICAL CHEMISTRY B
(2009)
Article
Chemistry, Physical
Sheng-You Huang, Sam Z. Grinter, Xiaoqin Zou
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2010)
Article
Biochemistry & Molecular Biology
Sheng-You Huang, Chengfei Yan, Sam Z. Grinter, Shan Chang, Lin Jiang, Xiaoqin Zou
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2013)
Article
Mathematics, Applied
P. Pfeifer, L. Aston, M. Banks, S. Barker, J. Burress, S. Carter, J. Coleman, S. Crockett, C. Faulhaber, J. Flavin, M. Gordon, L. Hardcastle, Z. Kallenborn, M. Kemiki, C. Lapilli, J. Pobst, R. Schott, P. Shah, S. Spellerberg, G. Suppes, D. Taylor, A. Tekeei, C. Wexler, M. Wood, P. Buckley, T. Breier, J. Downing, S. Eastman, P. Freeze, S. Graham, S. Grinter, A. Howard, J. Martinez, D. Radke, T. Vassalli, J. Ilavsky