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【分享】一步一步学计算机辅助药物设计【已搜索无重复】 - 药学...
来自 : muchong.com/html/201704/5776..
发布时间：2021-03-25
Hex http://www.biochem.abdn.ac.uk/hex/
Hex is an interactive protein docking and molecular superposition program. Cur rently, Hex understands protein and DNA structures in PDB format. Hex was writ ten by Dave Ritchie at the University of Aberdeen.
The main thing which distinguishes Hex from other macromolecular (i.e. protein and DNA) docking programs and molecular graphics packages is its use of spher ical polar Fourier correlations to accelerate docking calculations. The graphi cal nature of Hex came about largely because I wanted to visualise the results of such docking calculations in a natural and seamless way, without having to export unmanageably many (and usually quite big) coordinate files to one of t he many existing molecular graphics packages. For this reason, the graphical c apabilities in Hex are relatively primitive, although these days one can do qu ite a lot with a few calls to OpenGL. Nonetheless, if your main interest is in modelling macromolecular docking, Hex may have something new to offer!
Hardware Requirements Hex will run on most Silicon Graphics and Sun workstations and Linux PC machin es. The Linux PC versions are available for RedHat versions 7.0, 7.2, 7.3 and 8.0, but these should run under other Linux distributions.
注册后免费下载
还有许多大型的商业软件包里都有相关的软件，下面的目录比较完整
Protein-protein (peptide) docking 3D-Dock Suite [FTDock, RPScore and MultiDock] (BioMolecular Modeling, Cancer R esearch UK) Bielefeld Protein Docking [detects geometrical and chemical complementarities between surfaces of proteins and estimates docking positions] BiGGER [protein-docking algorithm; intergrated in chemera, a molecular graphi cs and modeling program for studying protein structures and interactions] (Bio Tecnol, S.A.) DOT [computation of the electrostatic potential energy between two proteins or other charged molecules] (San Diego Supercomputer Center) HEX [protein docking and molecular superposition program] (University of Aberd een) GRAMM - Global Range Molecular Matching [see also the database of Protein-Prot ein Decoys for the validation of energy functions and refinement procedures] ( SUNY)
Protein-ligand docking Affinity (Accelrys Inc.) AutoDock (The Scripps Research Institute) CombiBUILD [fragment-based docking; program created to aid the design of combi natorial libraries] (Sandia National Labs) DockVision (University of Alberta) FRED - Fast Rigid Exhaustive Docking [multiconformer docking program] (OpenEye ) FlexiDock (Tripos) FlexX (BioSolveIt GmbH) GLIDE (Schr ouml;dinger GmbH) GOLD (CDSD) HINT! - Hydropathic Interactions (Virginia Commonwealth University) LIGPLOT [program for automatically plotting protein-ligand interactions] (Univ ersity College of London) SITUS 2.0 [program package for modeling of atomic resolution structures into l ow-resolution density maps] (Scripps Research Institute) VEGA [calculation of ligand-receptor interaction energy] (Milan University)
Protein-protein and protein ligand docking DOCK (UCSF Molecular Design Institute) ICM-Dock (MolSoft LLC)
8. 最后要看一下3D结构，可以用下面这些可视化软件 DS ViewerPro 5.0 最好的结构分子观看软件 有了这个软件，你还用cn3D么？
Accelrys\'\' Discovery Studio ViewerPro (DS ViewerPro) combines state of t he art molecular graphics with a full range of Windows reg; desktop integratio n tools. Using the DS ViewerPro you can visualize and share molecular informat ion in a clear and consistent way, whether it\'\'s by exchanging chemical files o r by including dynamic chemical structures in Word documents, spreadsheets, or presentations
http://www.accelrys.com/dstudio/ds_viewer/
Analyzing Molecular Models Next: Accessing DataAnalysis and measurement tools help you to evaluate geomet ry and understand chemistry. Discovery Studio ViewerPro automatically c alculates atomic and molecular properties for molecules sketched or read in. M easurement monitors can be created, all of which are completely dynamic. As yo ur modeling environment changes, your monitors are automatically recalculated. The DS ViewerPro includes additional analysis features. For example, you coul d investigate potential hydrogen bonds or compute a solvent-accessible surface for a protein structure.
Computational Features: Calculate:Number of atoms Molecular formula Molecular weight Exact molecular weight Molecular volume Partial charge Measureistances Angles Dihedrals Angles Compute: 3D geometry from 2D Surfaces Chirality Protein secondary structure Hydrogen bonds Bumps (contacts between nonbonded atoms)
Rasmol Rasmol http://www.umass.edu/microbio/rasmol/
非常经典的观看生物分子3D结构的软件，免费下载
Chime MDL Chime
http://www.mdlchime.com/chime/ IE与NetScape浏览器插件,安装后,可以直接用浏览器观看PDB格式的文件,直接在浏览器中 观看3D分子。不需RASMOL。 免费下载
9. 再单独介绍几个软件 1. ICM 功能强大的icm ICM http://www.molsoft.com/
*Building and validating structural models of protein targets *Identifying biological ligand binding sites or new sites for allosteric regul ation of a protein of interest. *Evaluating and ranking drug targets, including protein-protein interaction in terfaces, designing strategies for rational drug design *Screening virtual libraries of millions of compounds using the revolutionary Molsoft flexible docking and scoring procedure. *Identifying interaction hot-spots, i.e. the candidate amino-acid positions in volved in protein-protein interactions *Predicting loop conformations in proteins *Designing proteins with desired properties *Docking flexible peptides to proteins *Designing peptides blocking protein-protein interactions *2D to 3D conversion, analysis and clustering of large compound libraries, *Predicting compound properties, building QSAR models, 3D pharmacophore constr uction and search.
windows下的软件 上官方网站就知道功能有多么强大,不过一般用户没法得到
免费的icm资源 ICM拿不到,但还有些免费的资源可以用一下
Abagyan Lab http://abagyan.scripps.edu/lab/web/man/frames.htm 据说是ICM的老家,里面有Homology Modeling Server ,可以免费使用,感觉还不错
Molsoft http://www.molsoft.com/ 官方网站上有两个在线小工具,PDB Viewer 和2D to 3D Molecular Converter 可以使用
ICM Lite ICM的简化版,免费推出,不过现在官方网站不提供下载了,但可以用google或天网搜一下,说 不定还能找到
Hex is an interactive protein docking and molecular superposition program. Cur rently, Hex understands protein and DNA structures in PDB format. Hex was writ ten by Dave Ritchie at the University of Aberdeen.
The main thing which distinguishes Hex from other macromolecular (i.e. protein and DNA) docking programs and molecular graphics packages is its use of spher ical polar Fourier correlations to accelerate docking calculations. The graphi cal nature of Hex came about largely because I wanted to visualise the results of such docking calculations in a natural and seamless way, without having to export unmanageably many (and usually quite big) coordinate files to one of t he many existing molecular graphics packages. For this reason, the graphical c apabilities in Hex are relatively primitive, although these days one can do qu ite a lot with a few calls to OpenGL. Nonetheless, if your main interest is in modelling macromolecular docking, Hex may have something new to offer!
Hardware Requirements Hex will run on most Silicon Graphics and Sun workstations and Linux PC machin es. The Linux PC versions are available for RedHat versions 7.0, 7.2, 7.3 and 8.0, but these should run under other Linux distributions.
注册后免费下载
还有许多大型的商业软件包里都有相关的软件，下面的目录比较完整
Protein-protein (peptide) docking 3D-Dock Suite [FTDock, RPScore and MultiDock] (BioMolecular Modeling, Cancer R esearch UK) Bielefeld Protein Docking [detects geometrical and chemical complementarities between surfaces of proteins and estimates docking positions] BiGGER [protein-docking algorithm; intergrated in chemera, a molecular graphi cs and modeling program for studying protein structures and interactions] (Bio Tecnol, S.A.) DOT [computation of the electrostatic potential energy between two proteins or other charged molecules] (San Diego Supercomputer Center) HEX [protein docking and molecular superposition program] (University of Aberd een) GRAMM - Global Range Molecular Matching [see also the database of Protein-Prot ein Decoys for the validation of energy functions and refinement procedures] ( SUNY)
Protein-ligand docking Affinity (Accelrys Inc.) AutoDock (The Scripps Research Institute) CombiBUILD [fragment-based docking; program created to aid the design of combi natorial libraries] (Sandia National Labs) DockVision (University of Alberta) FRED - Fast Rigid Exhaustive Docking [multiconformer docking program] (OpenEye ) FlexiDock (Tripos) FlexX (BioSolveIt GmbH) GLIDE (Schr ouml;dinger GmbH) GOLD (CDSD) HINT! - Hydropathic Interactions (Virginia Commonwealth University) LIGPLOT [program for automatically plotting protein-ligand interactions] (Univ ersity College of London) SITUS 2.0 [program package for modeling of atomic resolution structures into l ow-resolution density maps] (Scripps Research Institute) VEGA [calculation of ligand-receptor interaction energy] (Milan University)
Protein-protein and protein ligand docking DOCK (UCSF Molecular Design Institute) ICM-Dock (MolSoft LLC)
8. 最后要看一下3D结构，可以用下面这些可视化软件 DS ViewerPro 5.0 最好的结构分子观看软件 有了这个软件，你还用cn3D么？
Accelrys\'\' Discovery Studio ViewerPro (DS ViewerPro) combines state of t he art molecular graphics with a full range of Windows reg; desktop integratio n tools. Using the DS ViewerPro you can visualize and share molecular informat ion in a clear and consistent way, whether it\'\'s by exchanging chemical files o r by including dynamic chemical structures in Word documents, spreadsheets, or presentations
http://www.accelrys.com/dstudio/ds_viewer/
Analyzing Molecular Models Next: Accessing DataAnalysis and measurement tools help you to evaluate geomet ry and understand chemistry. Discovery Studio ViewerPro automatically c alculates atomic and molecular properties for molecules sketched or read in. M easurement monitors can be created, all of which are completely dynamic. As yo ur modeling environment changes, your monitors are automatically recalculated. The DS ViewerPro includes additional analysis features. For example, you coul d investigate potential hydrogen bonds or compute a solvent-accessible surface for a protein structure.
Computational Features: Calculate:Number of atoms Molecular formula Molecular weight Exact molecular weight Molecular volume Partial charge Measureistances Angles Dihedrals Angles Compute: 3D geometry from 2D Surfaces Chirality Protein secondary structure Hydrogen bonds Bumps (contacts between nonbonded atoms)
Rasmol Rasmol http://www.umass.edu/microbio/rasmol/
非常经典的观看生物分子3D结构的软件，免费下载
Chime MDL Chime
http://www.mdlchime.com/chime/ IE与NetScape浏览器插件,安装后,可以直接用浏览器观看PDB格式的文件,直接在浏览器中 观看3D分子。不需RASMOL。 免费下载
9. 再单独介绍几个软件 1. ICM 功能强大的icm ICM http://www.molsoft.com/
*Building and validating structural models of protein targets *Identifying biological ligand binding sites or new sites for allosteric regul ation of a protein of interest. *Evaluating and ranking drug targets, including protein-protein interaction in terfaces, designing strategies for rational drug design *Screening virtual libraries of millions of compounds using the revolutionary Molsoft flexible docking and scoring procedure. *Identifying interaction hot-spots, i.e. the candidate amino-acid positions in volved in protein-protein interactions *Predicting loop conformations in proteins *Designing proteins with desired properties *Docking flexible peptides to proteins *Designing peptides blocking protein-protein interactions *2D to 3D conversion, analysis and clustering of large compound libraries, *Predicting compound properties, building QSAR models, 3D pharmacophore constr uction and search.
windows下的软件 上官方网站就知道功能有多么强大,不过一般用户没法得到
免费的icm资源 ICM拿不到,但还有些免费的资源可以用一下
Abagyan Lab http://abagyan.scripps.edu/lab/web/man/frames.htm 据说是ICM的老家,里面有Homology Modeling Server ,可以免费使用,感觉还不错
Molsoft http://www.molsoft.com/ 官方网站上有两个在线小工具,PDB Viewer 和2D to 3D Molecular Converter 可以使用
ICM Lite ICM的简化版,免费推出,不过现在官方网站不提供下载了,但可以用google或天网搜一下,说 不定还能找到
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发布于 ： 2021-03-25
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