Visual Analysis of protein-ligand interactions

被引：14
作者：
Vazquez, P. [1 ]
Hermosilla, P. [2 ]
Guallar, V. [3 ,4 ]
Estrada, J. [3 ]
Vinacua, A. [1 ]
机构：
[1] Univ Politecn Cataluna, ViRVIG Grp, Barcelona, Spain
[2] Univ Ulm, Visual Comp Grp, Ulm, Germany
[3] Barcelona SuperComp Ctr, Barcelona, Spain
[4] ICREA, Barcelona, Spain
来源：
COMPUTER GRAPHICS FORUM | 2018年 / 37卷 / 03期
关键词：
OF-THE-ART; PHOSPHOLIPASE A(2); VISUALIZATION; COMPLEX; TOOL; RESOLUTION; DIAGRAMS; CRYSTAL; TUNNELS; BINDING;
D O I：
10.1111/cgf.13428
中图分类号：
TP31 [计算机软件];
学科分类号：
081202 ; 0835 ;
摘要：
The analysis of protein-ligand interactions is complex because of the many factors at play. Most current methods for visual analysis provide this information in the form of simple 2D plots, which, besides being quite space hungry, often encode a low number of different properties. In this paper we present a system for compact 2D visualization of molecular simulations. It purposely omits most spatial information and presents physical information associated to single molecular components and their pairwise interactions through a set of 2D InfoVis tools with coordinated views, suitable interaction, and focus+context techniques to analyze large amounts of data. The system provides a wide range of motifs for elements such as protein secondary structures or hydrogen bond networks, and a set of tools for their interactive inspection, both for a single simulation and for comparing two different simulations. As a result, the analysis of protein-ligand interactions of Molecular Simulation trajectories is greatly facilitated.
引用
收藏
页码：391 / 402
页数：12
相关论文
共 42 条
[1]   Integrated modeling program, applied chemical theory (IMPACT) [J].
Banks, JL ;
Beard, HS ;
Cao, YX ;
Cho, AE ;
Damm, W ;
Farid, R ;
Felts, AK ;
Halgren, TA ;
Mainz, DT ;
Maple, JR ;
Murphy, R ;
Philipp, DM ;
Repasky, MP ;
Zhang, LY ;
Berne, BJ ;
Friesner, RA ;
Gallicchio, E ;
Levy, RM .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1752-1780
[2]   Generalized born models of macromolecular solvation effects [J].
Bashford, D ;
Case, DA .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 2000, 51 :129-152
[3]   MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids [J].
Byska, J. ;
Jurcik, A. ;
Groeller, M. E. ;
Viola, I. ;
Kozlikova, B. .
COMPUTER GRAPHICS FORUM, 2015, 34 (03) :1-10
[4]   AnimoAminoMiner: Exploration of Protein Tunnels and their Properties in Molecular Dynamics [J].
Byska, Jan ;
Le Muzic, Mathieu ;
Groller, M. Eduard ;
Viola, Ivan ;
Kozlikova, Barbora .
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2016, 22 (01) :747-756
[5]   LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions [J].
Caboche, Segolene .
JOURNAL OF CHEMINFORMATICS, 2013, 5
[6]   Dynamical Non-Equilibrium Molecular Dynamics [J].
Ciccotti, Giovanni ;
Ferrario, Mauro .
ENTROPY, 2014, 16 (01) :233-257
[7]   Molecular surface abstraction [J].
Cipriano, Gregory ;
Gleicher, Laichael .
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2007, 13 (06) :1608-1615
[8]  
Cui Y., 2016, BIOINFORMATICS
[9]   Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing [J].
Falk, Martin ;
Krone, Michael ;
Ertl, Thomas .
COMPUTER GRAPHICS FORUM, 2013, 32 (08) :195-206
[10]   Visualization of Signal Transduction Processes in the Crowded Environment of the Cell [J].
Falk, Martin ;
Klann, Michael ;
Reuss, Matthias ;
Ertl, Thomas .
IEEE PACIFIC VISUALIZATION SYMPOSIUM 2009, PROCEEDINGS, 2009, :169-+
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