Molecular Modeling Software fwd

Maybe too many, select the proper one is also challenging!!

modeling software (collected at http://www.mybiosoftware.com).

3DNA 2.0 – Vsualization of Three-Dimensional Nucleic Acid Structures

ActiveICM 1.1.6 – PowerPoint & Web Browsers Plugin to Display 3D Modules

AlloPathFinder 1.1 – Compute Likely Allosteric Pathways in Proteins

AlphaMol 1.0 – Tools for Biomolecular Geometry

AMBER 11 – Assisted Model Building with Energy Refinement

AmberTools 1.5 – Molecular Dynamics Simulation

ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files

APBS 1.3 – Evaluat Electrostatic Properties of Nanoscale Biomolecular System

ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program

Ascalaph 1.7.12 – Molecular Modelling Suite

AtVol 1.2 – Atomic Volume Calculation

AUDocker v1 – GUI for AutoDock Vina

Autobondrot 2.0 – Generate Multiple Molecular Conformation

AutoDock 4.2.3 / 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 2.0.4 – Use AutoDock Vina in Protein Inhibitor Design

Avogadro 1.0.3 – Molecule Editor & Visualizer

AVP 1.3 – Calculate Protein Void Volumes and Packing Quality

AxPyMOL 1.0r1 – PowerPoint Plug-In for Embedding 3D Molecular Images & Animations

B 1.0alpha – Biomolecular Modeling Package

BALLView 2.0-r1 – Molecular Modeling & Visualization

Benchware® 3D Explorer 2.6 – 3D Chemical Visualization

Bioclipse 2.4 – Life Sciences Workbench

Biodesigner 0.75 – Molecular Modeling & Visualization

BioEditor 1.6.1 – Present Macromolecular Structure & Structural Annotation

BioViewer 1.5.7 – Read only version of BioEditor

Biskit 2.3.1 – Python Platform for Structural Bioinformatics

BndLst 1.6 – List Covalent & H-bonded Neighboring Atoms

C2A 1.0 – Coarse to Atomic

CCOMP 3.70 – Compare Ligand/Receptor Complexes

CHARMM 36 – Macromolecular Dynamics and Mechanics

ChemCraft 1.6 – Graphical Program for working with Quantum Chemistry Computation

Chemis3D 2.89b – Java 3D Molecular Viewer Applet

Chemitorium 3.5 – Molecule Editor & 3D Chemical Structure Viewer

Chime 2.6SP8 – Display 2D / 3D Molecules directly in Web Pages

ClashList 1.1 – Build Lists of van der Waals Clashes from PDB file

ClashScore 1.1 – R Script for VTF Percentile Plot

CLICK – Comparison of Biomolecular 3D Structures

Cluster 1.3 – Build Collections of Interacting Items

CN3D 4.3 – 3D Molecular Structure Viewer

CompuCell3D 3.6.0 – 3D Multiscale Multi-cell Simulations

Concoord 2.1 – Protein Structure Generation from Distance Constraint

CONSCRIPT – Generate Electron Density Isosurfaces in Protein Crystallography

Coot 0.6.2 – Macromolecular Model Building Tool

COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures

CueMol 2.0.1.161 – Macromolecular Structure Visualization

Dang 1.8 – Read PDB File & Generate Geometric Measurement Table

Dangle 0.63 – Read PDB File & Generate Geometric Measurement Table

DeepView 4.04 – Analyze Several Proteins 3D Structure at the Same Time

Desmond 2.4 – High-speed Molecular Dynamics Simulation

DINO 0.9.4 – Structural Biology Data 3D Visualization

DireX 0.5 – Low-resolution Structure Refinement

DOCK 6.4 – Docking Molecules to each other

DS Visualizer 3.1 & ActiveX Control 3.1 – Molecular Visualization

DTMM 4.2 – molecular modelling program

EDTSurf – Quick and Accurate Construction of Macromolecular Surfaces

EGO VIII – Molecular Dynamics Simulation

eMovie 1.04 – Make Molecular Movies

Facio 15.1.1 – 3D-Graphics program for Molecular Modeling and Visualization

FEATURE 2.0 – Examine Biological Structures

FiltRest3D – Filtering Protein Models by Fuzzy Restraints

FINDSITE 1.0 – Ligand-binding Site Prediction & Functional Annotation

FINDSITE-LHM 1.0 – Homology Modeling Approach to Flexible Ligand Docking

Flex-EM – Fitting and Refinement of Atomic Structures

FlexS 2.0.0 – Predict Ligand Superpositions

Flipkin 2.4 – Script to Make the Kinemages

FMA 0901 – Protein Functional Mode Analysis

FREEHELIX 98 – Analyze DNA bending

FRETsg 1.0 – Structure Building from Multiple FRET Distances

Friend 2.0 – Multiple Structure Visualization & Multiple Sequence Alignment

FTDock 2.0/ RPScore /MultiDock 1.0 – Protein Molecule 3D-Dock Suite

g0penMol 3.0 – Molecules Visualization & Analysis

Gabedit 2.4.0 – Graphical User Interface to Computational Chemistry Packages

GAP 1.2.14 – Geometric Analysis of Proteins

GDIS 0.90 – Visualization Program for Molecular and Periodic Systems

Ghemical 2.99.2 – Molecular Modeling and Editing Package for GNOME

GPGPUFRAGFOLD 0.1 – CUDA Fragment Assembly Based Protein Structure Prediction

Graphite-MicroMégas – Model in 3D Assemblies of Proteins and DNA

GROMACS 4.5.4 – Molecular Simulation

Gromita 1.06 – GUI for GROMACS

g_correlation 1.02 – Generalized Correlation for Biomolecular Dynamics

g_permute 1.12 – Permutation-Reduced Phase Space Density Compaction

HAAD – Quick and Accurate Hydrogen Atom Addition

Hollow 1.1 – Illustration software for Proteins

ICM-Browser 3.7 2b – Molecules & sequence alignments Visualization

iMol 0.40 – Molecular Visualization Application for Mac OS X

iMolview 1.1 – iPhone & iPad App for Browsing Protein, DNA & Drug Molecules in 3D

IMP 1.0 – Integrative Modeling Platform

ISD 1.1 – Bayesian NMR Structure Calculation

ISIM – Simulation of Ions in the Grand Canonical Ensemble

ISIM Interface 1.3.2 – Graphical Interface for running the program

ISIM

Jamberoo 11 – Cross-Platform Molecular Editor & Builder

Jimp 2 0.091 – Visualize and Manipulate Molecules

Jmol 12.0.50 – Java Viewer for Chemical Structures in 3D

JMVS 4 041122 – Java3D Molecular Visualisation System

jSim for Gromacs 0.63b – Graphical User Interface for Gromacs

JyMOL 1.0 – Java-based Molecular Visualization

Kin2Dcont 1.8 & Kin3Dcont 1.12 – Produce Molecule Contour Map

KiNG 2.20 – Three Dimensional Vector Graphics

KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment

LGscore/LGscore2 2.0 – Measure Quality of Protein Model

LifeExplorer 20100108 – 3D Navigation Tool for Cells

LigandScout 3.02 – Pharmacophore 3D Modeling

LoopTK 2.0.1 – Protein Loop Kinematic Toolkit

lrrr 1.4 beta1 – Determines Ligands on the Surface of Proteins

Mage 6.47 – Kinemage File 3D Display

Maptools 1.0 – Deal with Experimental (X-ray, EM) 3D Maps

MapVol 1.1 – Awk Script to Assign Volume by Atom

MaSK 1.3.0 – Molecular Modeling and Simulation Kit

MD Morphing 1.0 – Perform Molecular Dynamics Morphing Simulations

MDynaMix 5.2 – Molecular Dynamics Program

MetaTASSER – Protein Structure Prediction tool

MGLTools 1.5.6RC2 – Visualization & Analysis of Molecular Structures

MINT 3.2 – User Interface to Modeller

MMB 2.4 – Model the Structure and Dynamics of Macromolecules

mmPDBViewer 2009.3.20.4 – Protein Data Bank Viewer

MMPRO 0.7 – Molecule Visualization & Analysis Program

MMTK 2.7.4 – The Molecular Modelling Toolkit

MMTSB toolset – Multiscale Modeling Tools for Structural Biology

MMV 2.2.0 – Visualization of Molecules

ModeHunter 1.1 – Normal Mode Analysis of Coarse Grained Elastic Networks

MODELLER 9.10 – Comparative Protein Structure Modeling

Models@Home 4.5 – Distributed Computing Software for Protein Modeling

ModeRNA 1.6 – Comparative RNA 3D Modeling

ModPipe 2.2.0 – Calculate Protein Structure Model

ModRefiner 20111024 – High-resolution Protein Structure Refinement

ModView 0.903 – Visualization of Multiple Protein Sequences & Structures

MOIL 12.0.3671 – Molecular Modeling Software

Móilín 2011 – Molecular Modelling Software

Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion

MOLA – System for Virtual Screening using AutoDock4/Vina on Computer Clusters

MolIDE 1.7 – Protein 3D Homology Modeling

MolPOV 2.0.8 – PDB to POV File Converter & Visualizer

MolScript 2.1.2 – Display Molecular 3D Structures

MolTalk 3.0.1 – Computational Environment for Structural Bioinformatics

MoluCAD 1.034 – Molecular Modeling & Visualization Tool

MoSART pr – NMR-based Biomolecular Structure Computation

MSMExplorer 0.02 – Visualization Application for Markov State Models for Folding

MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing

NAContacts 2.5 – Write Contact Information between Nucleic Acid Bases

NAST 1.0 – Nucleic Acid Simulation Tool

NMFF – Normal Mode Flexible Fitting

NOC 3.01 – Molecular Explorer for Protein Structure Visualization

OB Score 1.0 – Structural Genomics Target Ranking

OpenAstexViewer 3.0 – Software for Molecular Visualisation

OpenMM 3.1.1 – Library for Molecular Modeling Simulation

OpenMM Zephyr 2.0.3 – Molecular Simulation Application

OpenStructure 1.1.0 – Computational Structural Biology Framework

ORTEP-III 1.03 – Crystal Structure Illustration

Oscail 2011 – Crystallography & Molecular Modelling

OVOP 1.0 – View Generation for Protein Structures

PaDEL-ADV 1.6 – Facilitate Virtual Screening with AutoDock Vina

PDB Editor 090203 – PDB (Protein Data Bank) File Editor

PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats

PDBlib 2.2 – C++ Macromolecular Class Library

PDBpy – Python Parser for PDB files

PeppeR 0.8.160 – Graphical 3D-EM DAS Client

PHENIX 1.7 – Python-based Hierarchical ENvironment for Integrated Xtallography

PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter

Prekin 6.51 – Prepares Kinemages Files from PDB-format Files

PREPI 0.9 – Molecular 3D Representation

Probe 2.12 – Evaluate Atomic Packing & Contact Analysis

ProbeWithO 0.9.0 – Use Small Probe Contact Dots Within O

ProFit 3.1 – Protein Least Squares Fitting

ProSa 2003 – Protein Structure Research Tool

PROTEAND 1.0 – Display Macromolecular Structural Uncertainty

Protein Explorer 2.80 – Visualize 3D Structures of Macromolecules

ProteinGlimpse 1.6 – Visualize Macromolecules Retrieved from PDB

ProteinScope 1.0.5 – 3D Protein Structure Viewer

ProteinShader beta 0.9.4 – Illustrative Rendering of Macromolecules

ProtoMol 3.3 – Molecular Dynamics (MD) Simulation

PULCHRA 3.06 – All-atom Reconstruction & Refinement of Reduced Protein Models

pymacs 0.4 – Python Module for Dealing with Structure files from GROMACS

PyMOL 1.4.1 – Molecular Visualization System

PyOpenMM 3.0 – Python API of OpenMM Library

PyRx 0.8 – Virtual Screening software for Computer-Aided Drug Design

QTree 2.3 – Graphics Rendering using Quad-tree Algorithm

QuickPDB 20021101 – Java Applet for quickly viewing PROTEIN PDB Structure

QuteMol 0.41 – Molecular Visualization System

R.E.D. III.4 – Calculate RESP Charges

Ramachandran Plot Explorer 1.0 – Interactive Cross-platform Protein Viewer

Rasmol 2.7.5.2 – Molecular Graphics Visualisation

Raster3D 3.0-2 – Generate High Quality Raster Images of Proteins or other Molecules

RasTop 2.2 – Molecular Visualization Software Adapted for Rasmol

RDCvis 1.02 – Residual Dipolar Coupling Visualizer

Reduce 3.14 – Add Hydrogens to PDB Molecular Structure File

Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats

REMO 1.0 – Construct Full-atom Protein Models from C-alpha Traces

Ribbons 3.32 – Molecular Graphics Software

RIP 1.0 – Accelerated Molecular Dynamics

RNABC 1.11 – RNA Backbone Correction

Rosetta@home – Grid Software for Protein Folding

rTools 0.7.2 – PyMOL plugins

ScoreDotsAtAtom 1.0 – Bookkeep All-atom Contact Dot

Sculptor 2.0.2 – Docking & Visualization for Atomic Structures

SEQMOL 3.4.6 – Sequence Alignment & PDB Structure Analysis Utility

SHIFTS 4.3 – Predict Nitrogen, Carbon & Proton Chemical Shifts in Proteins

SimTK Core 2.1 – Simbios Biosimulation ToolKit

Situs 2.6 – Integration of Multi-Resolution Structures

Solvate 1.0 – Construct Atomic Solvent Environment Model for Given Atomic Macromolecule Model

StrukEd – Editor for Molecules & 3D Viewer

Suitename 0.3 – RNA Conformer

Superficial 1.2 – Identification of Potential Epitopes or Binding Sites

SuperMimic – Fit Peptide Mimetics into Protein Structures

TASSER-Lite 1.0 – Protein Structure Modeling tool

tCONCOORD 1.0 – Predict Protein Conformational Flexibility

Tessellator 1.0 – Software for Tessellation of 3D Volume in Biological Molecule

Theseus 1.6.1 – Superimpose Macromolecular Structures

THREADER 3.51 – Protein Fold Recognition by Threading

TimeScapes 1.2.2 – Molecular Dynamics Analysis tool

Tinker 5.1.09 – Software Tools for Molecular Design

Torsions – Calculates Backbone Torsion Angles from a PDB file

UCSF Chimera 1.5.3 – Molecular Modeling System

VcPpt – Protein Ligend Docking & in silico High-throughput Screening

VEGA ZZ 2.4.0 – Molecular Modeling Toolkit

VESTA 3.0 – 3D Visualization System for Electronic & Structural Analysis

Viewmol 2.4.1 – Molecule Viewer

ViewMol3D 5.00.alpha.3 – 3D OpenGL Viewer for Molecular Structures

VisProt3DS 3.03 – Stereoscopic Visual Analyzer of Biological Macromolecules

VMD 1.9 – Molecular Graphics Viewer

Voronoia 1.0 – Analyse Packing of Protein Structures

WebMol – JAVA PDB Viewer

WPDB 2.2 – The Protein Data Bank Through Windows

XCrySDen 1.5.24 – Crystalline & Molecular Structure Visualisation

XmMol 3.1 – Macromolecular Visualization and Modeling tool

XtalView 4.0 – Molecular Graphics Program

YAKUSA – Scan Structural database with Query Protein Structure

YASARA 11.9.18 – Molecular Graphics, Modeling & Simulation program

YUP 1.080827 / Yammp 2 – Molecular Simulation

Zodiac 0.6.5 – Molecular Modelling suite for Drug Design

HyperBalls Viewer – Molecular structures and trajectories visualization using GPU rendering