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Title:	Bioinformatics Softwares List
Website:	http://www.mybiosoftware.com/biology-software-list
Sort:	Useful tools
Description:	3D Molecular Models 1.1.2 - Manipulate 3D Models of Molecules for Android 3D-DART - DNA Structure Modelling Server 3D-Garden 1.4 - Protein-protein and Protein-polynucleotide Docking 3DCA - 3D Cluster Analysis 3DLigandSite - Ligand Binding Site Prediction Server 3Dmol.js - Molecular Visualization with WebGL 3DNA 2.2 - Vsualization of Three-Dimensional Nucleic Acid Structures 3V 1.3 - Volume Related Calculations ABS-Scan - Webserver for Insilico Binding site Alanine Scanning Mutagenesis ActiveICM 1.2-2 - PowerPoint & Web Browsers Plugin to Display 3D Modules Adepth - Measures of Atomic Depths in Macromolecules ADP_EM 1.03 - Fast Rigid-body Fitting Adun 0.81 - Biomolecular Simulator AIDA - Ab Initio Domain Assembly Server Al-Eigen - Contact Map Overlap by Alignment of Eigenvectors AlloPathFinder 1.1 - Compute Likely Allosteric Pathways in Proteins AlloPred 1.0.0 - Prediction of Allosteric Pockets on Proteins ALMOST 2.1.0 - Molecular Simulation toolkit for Protein Structure Determination AlphaMol 1.0 - Tools for Biomolecular Geometry AMBER 14 - Assisted Model Building with Energy Refinement AmberTools 14 - Molecular Dynamics Simulation AMMOS / DG-AMMOS - Automated Molecular Mechanics Optimization tool for in silico Screening / using Distance Geometry AMMP 2.0 - Molecular Mechanics, Dynamics and Modeling program ANGULATOR - Angular Trends Of Repeat Proteins ANOLEA 2.4.2-2 - Assess the Quality of a 3D Protein Structure ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files APBS 1.4.1 - Evaluat Electrostatic Properties of Nanoscale Biomolecular System aPPRove - Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding ArchiP 2.3 - Detecting Architectures of all-β and α/β-classes ArgusLab 4.0.1 - Molecular Modeling, Graphics & Drug Design Program ARP/wARP 7.5 - Crystallographic Macromolecular Model Building ArShift - Structure Based Predictor of Protein Aromatic Side-Chain Proton Chemical Shifts Ascalaph 1.8.88 - Molecular Modelling Suite Athena - Molecular visualisation software for Solaris Atomdroid 1.5.0 - Molecular Viewer/Builder for Android ATSAS 2.6.0 - program suite for Small-angle Scattering data analysis from Biological Macromolecules AtVol 1.2 - Atomic Volume Calculation AUDocker 1.1.2 - GUI for AutoDock Vina AuPosSOM 2.1 - Virtual Screening tool for the Automatic Analysis of Docked Structures Autobondrot 2.0 - Generate Multiple Molecular Conformation AutoChrom3D v1 - Modeling and Visualization the 3D Structure of Human or Mouse Chromatin AutoDock 4.2.6 / AutoDockTools 1.5.6 - Suite of Automated Docking Tools AutoDock Vina 1.1.2 - Molecular Docking and Virtual Screening Program Autodock/Vina plugin for PyMOL AutoGrow 3.0 - Use AutoDock Vina in Protein Inhibitor Design Avogadro 2.0.8.0 - Molecule Editor & Visualizer AVP 1.3 - Calculate Protein Void Volumes and Packing Quality AxPyMOL 1.7.4 - PowerPoint Plug-In for Embedding 3D Molecular Images & Animations B 1.0alpha - Biomolecular Modeling Package BALBES 1.1.5 - Molecular Replacement ballaxy - Galaxy-based workflow toolkit for Structural Bioinformatics Balloon 1.6.3.1249 - Creates 3D Atomic Coordinates from Molecular Connectivity BALLView 1.4.79 - Molecular Modeling & Visualization BARNACLE 0.21 - RNA 3D Structure Prediction BASILISK 0.1 - Probabilistic Model of Side Chains in Proteins BD_BOX 1.2 - Brownian Dynamics Simulation BDOCK - Grid-based Protein-protein Docking software Benchware® 3D Explorer 2.7 - 3D Chemical Visualization BEST 3.1 - Macromolecular Crystallography BetaMol v0.92d - Molecular Modeling, Analysis, and Processing software BetaVoid v1 - Molecular voids via beta-complexes and Voronoi diagrams BINANA 1.0.2 - Analyzing Ligand Binding Bio3D 2.2-2 - Biological Structure Analysis BioBlender 1.0 - Software built on the Open-source 3D Modeling software Blender Bioclipse 2.6.1 - Life Sciences Workbench Biodesigner 0.75 - Molecular Modeling & Visualization BioEditor 1.6.1 - Present Macromolecular Structure & Structural Annotation BioShell 2.2 - Structural Biology Computation BioSuper - Superimposition of Biological Assemblies BioViewer 1.5.7 - Read only version of BioEditor Biskit 2.4.0 - Python Platform for Structural Bioinformatics BndLst 1.6 - List Covalent & H-bonded Neighboring Atoms BnP 1.02 - Protein Structure-determination package Bodil 0.8.1 - Biomolecular Visualization and Modeling BRAGI 20091106 - A Protein Visualization and Modeling Program BSP-SLIM - Low-Resolution Docking on Predicted Structures buccaneer 1.5 - Electron Density Interpretation/Protein Model Building software C2A 1.0 - Coarse to Atomic C2S 1.3 - Contact Map-based Protein Structure Reconstruction Pipeline CABS-flex - Server for fast Simulation of Protein Structure Fluctuations CABS-fold - Server for de novo and Consensus-based prediction of Protein Structure CAD-score 20140827 - Evaluation of Protein Structural Models against the Reference Structure Cadnano 2.5 - Design Three-dimensional DNA Origami Nanostructures CafeMol 2.1 - Biomolecular Modeling and Simulation Software CAVER 3.02 / CAVER Analyst 1.0 - software tool for Protein Analysis and Visualization CCBuilder 1.0 - Coiled-coil Protein Assemblies CCharPPI - Computational Characterisation of Protein-Protein Interactions CCOMP 3.70 - Compare Ligand/Receptor Complexes ccp4 6.5 - Macromolecular X-Ray Crystallography CCP4mg 2.9.0 - Create Publication Quality Molecular Images and Movies Cell-Dock - High-performance Protein-protein Docking cGRILL 0.5 - Unsophisticated but Effective Affinity Map Generator CH3Shift - Structure Based Prediction of Protein Methyl Group Chemical Shifts CHARMM 40 / CHARMM-GUI 1.7 - Macromolecular Dynamics and Mechanics / GUI CheckMyMetal - Metal Binding Site Validation Server Chem3D for iPad 2.0.2 - View and manipulate stunning 3D chemical and biochemical images ChemCraft b395 - Graphical Program for working with Quantum Chemistry Computation Chemis3D 2.89b - Java 3D Molecular Viewer Applet Chemitorium 4.0 - Molecule Editor & 3D Chemical Structure Viewer ChExVis - Molecular Channel Extraction and Visualization ClashList 1.1 - Build Lists of van der Waals Clashes from PDB file ClashScore 1.1 - R Script for VTF Percentile Plot CLC Drug Discovery Workbench 2.4 - Virtual Lab Bench for Chemists CLICK - Comparison of Biomolecular 3D Structures Cluster 1.3 - Build Collections of Interacting Items CMol 1.3.3 - Molecular Viewer for the iPad, iPhone and iPod touch CMView 1.1.1 - Protein Contact Map Visualization and Analysis CN3D 4.3.1 - 3D Molecular Structure Viewer CNSsolve 1.3 - X-ray Crystallography Suite CombDock - COMBinatorial Asembly by mutiple DOCKing COMBOSA3D 1.1 - Coloring Of Molecules Based On Sequence Alignment COMMA - Dissect Proteins Dynamical Architectures COMPLIG - Ligand Molecule Superposition tool COMPPDB - PDB Superposition Tool CompuCell3D 3.7.4 - 3D Multiscale Multi-cell Simulations Concavity 0.1 - Ligand Binding Site Prediction from Protein Sequence and Structure Concoord 2.1.2 - Protein Structure Generation from Distance Constraint CONFOLD 1.0 - Residue-residue Contact-guided ab initio Protein Folding CONSCRIPT - Generate Electron Density Isosurfaces in Protein Crystallography

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