MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions

被引：10
作者：
Bai, Bing [1 ,2 ]
Zou, Rongfeng [1 ,2 ,3 ]
Chan, H. C. Stephen [1 ,2 ]
Li, Hongchun [1 ,2 ]
Yuan, Shuguang [1 ,2 ,3 ]
机构：
[1] Chinese Acad Sci, Shenzhen Inst Adv Technol, 1068 Xueyuan Ave, Shenzhen 518055, Peoples R China
[2] Univ Chinese Acad Sci, Shenzhen Inst Adv Technol, 1068 Xueyuan Ave, Shenzhen 518055, Peoples R China
[3] AlphaMol Sci Ltd, 1068 Xueyuan Ave, Shenzhen 518055, Peoples R China
来源：
MOLECULES | 2021年 / 26卷 / 15期
基金：
中国国家自然科学基金;
关键词：
protein-ligand interaction; trajectory analysis; WebGL; web server; LIGAND INTERACTIONS; DATABASE; PREDICTION;
D O I：
10.3390/molecules26154625
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Protein-ligand interaction analysis is important for drug discovery and rational protein design. The existing online tools adopt only a single conformation of the complex structure for calculating and displaying the interactions, whereas both protein residues and ligand molecules are flexible to some extent. The interactions evolved with time in the trajectories are of greater interest. MolADI is a user-friendly online tool which analyzes the protein-ligand interactions in detail for either a single structure or a trajectory. Interactions can be viewed easily with both 2D graphs and 3D representations. MolADI is available as a web application.
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页数：10
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共 20 条
[11]   ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites [J].
Konc, Janez ;
Janezic, Dusanka .
NUCLEIC ACIDS RESEARCH, 2014, 42 (W1) :W215-W220
[12]   ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures [J].
Konc, Janez ;
Cesnik, Tomo ;
Trykowska Konc, Joanna ;
Penca, Mate ;
Janezic, Dusanka .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2012, 52 (02) :604-612
[13]   LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery [J].
Laskowski, Roman A. ;
Swindells, Mark B. .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 51 (10) :2778-2786
[14]   Pybel: a Python']Python wrapper for the OpenBabel cheminformatics toolkit [J].
O'Boyle, Noel M. ;
Morley, Chris ;
Hutchison, Geoffrey R. .
CHEMISTRY CENTRAL JOURNAL, 2008, 2 (1)
[15]   NGL viewer: web-based molecular graphics for large complexes [J].
Rose, Alexander S. ;
Bradley, Anthony R. ;
Valasatava, Yana ;
Duarte, Jose M. ;
Prlic, Andreas ;
Rose, Peter W. .
BIOINFORMATICS, 2018, 34 (21) :3755-3758
[16]   NGL Viewer: a web application for molecular visualization [J].
Rose, Alexander S. ;
Hildebrand, Peter W. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W576-W579
[17]   PLIP: fully automated protein-ligand interaction profiler [J].
Salentin, Sebastian ;
Schreiber, Sven ;
Haupt, V. Joachim ;
Adasme, Melissa F. ;
Schroeder, Michael .
NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W443-W447
[18]   CREDO: A Protein-Ligand Interaction Database for Drug Discovery [J].
Schreyer, Adrian ;
Blundell, Tom .
CHEMICAL BIOLOGY & DRUG DESIGN, 2009, 73 (02) :157-167
[19]   Automated analysis of interatomic contacts in proteins [J].
Sobolev, V ;
Sorokine, A ;
Prilusky, J ;
Abola, EE ;
Edelman, M .
BIOINFORMATICS, 1999, 15 (04) :327-332
[20]   PROLIX: Rapid Mining of Protein-Ligand Interactions in Large Crystal Structure Databases [J].
Weisel, Martin ;
Bitter, Hans-Marcus ;
Diederich, Francois ;
So, W. Venus ;
Kondru, Rama .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2012, 52 (06) :1450-1461
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