3D molecular model
- BioBlender 0.6 – Software built on the open-source 3D modeling software Blender
- Phaistos 1.0 – Proteins Structure Prediction
- BASILISK 0.1 – Probabilistic Model of Side Chains in Proteins
- BARNACLE 0.21 – RNA 3D Structure Prediction
- GalaxyDock 2 – Protein-ligand Docking program
- DireX 0.6 – Low-resolution Structure Refinement
- Jmol 13.0.15 / Jmol for Android 1.1 – Java Viewer for Chemical Structures in 3D
- OWL 2.0.1 – Java toolkit for Computational Structural Biology
- Ascalaph 1.8.54 – Molecular Modelling Suite
- CueMol 2.1.0.270 – Macromolecular Structure Visualization
- YASARA 13.4.21 – Molecular Graphics, Modeling & Simulation program
- Rosetta@home 3.46 – Grid Software for Protein Folding
- RCSB PDB Mobile 3.06 – Access to the RCSB PDB resources
- MolView 1.9 – 3D Stereo Visualizator for Android
- CrystalMaker 8.7.2 – Build Crystal & Molecular Structures
- ProDy 1.4.2 – Python package for Analysis and Modeling of Protein Structural Dynamics
- UCSF Chimera 1.8 – Molecular Modeling System
- OpenStructure 1.3.2 – Computational Structural Biology Framework
- PHENIX 1.8.2 – Python-based Hierarchical ENvironment for Integrated Xtallography
- ChemCraft b375 – Graphical Program for working with Quantum Chemistry Computation
- ICM-Browser 3.7 2e – Molecules & sequence alignments Visualization
- VEGA ZZ 3.0.1.22 – Molecular Modeling Toolkit
- PDBjViewer 4.3.1 – Display 3D Molecular Graphics of Proteins and Nucleic Acids
- CMView 1.1.1 – Protein Contact Map Visualization and Analysis
- 3DNA 2.1 – Vsualization of Three-Dimensional Nucleic Acid Structures
- DFprot 1.0 – Provide Deformability/Flexibily Analysis of 3D Structure
- ADP_EM 1.03 – Fast Rigid-body Fitting
- iMODFIT 1.02 – Fitting of Atomic Structures into EM maps based on iMOD
- iMOD 1.03 – Multipurpose Normal Mode Analysis in Internal Coordinates
- FRODOCK 1.04 – Fast Rotational DOCKing tool
- FoldX/Yasara 3.4.9 – FoldX plugin for Yasara
- Surface Racer 5.0 – Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature
- Balloon 1.4.0.1036 – Creates 3D Atomic Coordinates from Molecular Connectivity
- ShaEP 1.1.2.1036 – Align Two Rigid 3D Molecular Structure Models
- CCP4mg 2.7.3 – Create Publication Quality Molecular Images and Movies
- Situs 2.7.2 – Integration of Multi-Resolution Structures
- MDynaMix 5.2.5 – Molecular Dynamics Program
- MMB 2.11 – Model the Structure and Dynamics of Macromolecules
- Facio 16.4.2 – 3D-Graphics program for Molecular Modeling and Visualization
- ActiveICM 1.1-8 – PowerPoint & Web Browsers Plugin to Display 3D Modules
- VESTA 3.1.5 – 3D Visualization System for Electronic & Structural Analysis
- AUDocker 1.1.2 – GUI for AutoDock Vina
- MGLTools 1.5.6 – Visualization & Analysis of Molecular Structures
- AmberTools 13 – Molecular Dynamics Simulation
- Gromita 3.0 – GUI for GROMACS
- Concoord 2.1.2 – Protein Structure Generation from Distance Constraint
- Móilín 2013 – Molecular Modelling Software
- Oscail 2013 – Crystallography & Molecular Modelling
- Tinker 6.2 – Software Tools for Molecular Design
- R.E.D. III.52 – Calculate RESP Charges
- MOLE 2.0 – Location and Characterization of Channels, Tunnels and Pores in Molecular Structures
- BALLView 1.4.2 – Molecular Modeling & Visualization
- MOLDEN 5.0.6 – Package for Displaying Molecular Density
- DOCK 6.6 – Docking Molecules to each other
- MrBUMP 0.4.4 – Automated Molecular Replacement
- IMP 2.0.0 – Integrative Modeling Platform
- AutoGrow 3.0 – Use AutoDock Vina in Protein Inhibitor Design
- FMA 0901 – Protein Functional Mode Analysis
- Bioclipse 2.6 – Life Sciences Workbench
- Adepth – Measures of Atomic Depths in Macromolecules
- RNA2D3D 5.7.0 – Conversion of RNA 2D Structures to 3D and 3D Modeling
- OpenMM 5.0.1 – Library for Molecular Modeling Simulation
- PyMOL 1.6 – Molecular Visualization System
- Ionize 1.6.0 – Placement Atomic Ions around 3D Biomolecular Structure
- Dynamical Network Analysis – Characterizing Allosteric Signalling through Biomolecular Complexes
- PyPLIF 0.1.1 – Python-based Protein-Ligand Interaction Fingerprinting
- MSMExplorer 0.9 – Visualization Application for Markov State Models for Folding
- GROMACS 4.6.1 – Molecular Simulation
- SwarmDock – Webservice for Generating 3D Structures of Protein-protein complexes
- ProNOI – Protein Nano-Object Integrator
- FRETsg 1.0 – Structure Building from Multiple FRET Distances
- FTProd – Binding Site Comparison across Multiple Structures
- Garlic 1.6 – Free Molecular Viewer and Editor
- Gabedit 2.4.6 – Graphical User Interface to Computational Chemistry Packages
- MaxSprout 200610 – Reconstruction of 3D Coordinates from C(alpha) trace
- CAD-score 20121208 – Evaluation of Protein Structural Models against the Reference Structure
- Voroprot 0.7.6.7 – Explore Geomeric Features of Protein Structure
- SPADE 1.3 – Structural Proteomics Application Development Environment
- PocketMol 1.0 – Molecular Visualization Program for the Pocket PC
- ZMM 20120214 – Molecular Modeling program for Theoretical studies of systems of any complexity
- mMaya 1.2 – Molecular Maya toolkit
- CMol 1.3.3 – Molecular Viewer for the iPad, iPhone and iPod touch
- 3D Molecular Models 1.1.2 – Manipulate 3D Models of Molecules for Android
- Molecule Viewer 3D 1.2.5 – 3D Molecular Viewer for Android
- Atomdroid 1.5.0 – Molecular Viewer/Builder for Android
- GLmol 0.47 – Molecular Viewer on WebGL/Javascript
- ESmol 0.74 / NDKmol 0.92 – Molecular Viewer for Android
- MolView – Exploratory 3D Molecule Viewer
- Molecules 2.1 – iPhone / iPad Application for PDB Structures
- ANGULATOR – Angular Trends Of Repeat Proteins
- BRAGI 20091106 – A Protein Visualization and Modeling Program
- AutoDock 4.2.5.1 / AutoDockTools 1.5.6 – Suite of Automated Docking Tools
- BDOCK – Grid-based Protein-protein Docking software
- metaPPI – Meta Approach for Protein-protein Binding Sites Prediction
- metaPocket 2.0 – Meta approach for Protein Ligand-binding sites Prediction
- SCOWLP – Structural Classification of Protein Binding Regions
- MSPocket 1.1 – Detection and Graphical Analysis of Protein Surface Pockets
- MSMS 2.6.1 – Compute Molecular Surfaces
- ANOLEA 2.4.2-2 – Assess the Quality of a 3D Protein Structure
- LocalMove – Compute On-lattice Fits for Biopolymers
- Reveal – Viewer for Automated active-site Predictions for Polypeptides
- LSim 1.0.0 – Superposes Macromolecular Electron Densities and Computes Structural Similarity Score
- PDBHighlight 1.1.0 – A RasMol Script database
- Molekel 5.4.0 – 3D Molecular Visualization Program
- VeaR – Geometry-based Structural Highlighter for Polypeptides
- iMolview 1.6 – iPhone, iPad and Android App for Browsing Protein, DNA & Drug Molecules in 3D
- SEED 3.3.5 – Solvation Energy for Exhaustive Docking
- MMTK 2.7.8 – The Molecular Modelling Toolkit
- FlexS 2.1.2 – Predict Ligand Superpositions
- Theseus 2.0.1 – Superimpose Macromolecular Structures
- FlexV 1.9.0 – Molecular Visualization
- Models@Home 12.1 – Distributed Computing Software for Protein Modeling
- PeppeR 2.12 – Graphical 3D-EM DAS Client
- MOLARIS 9.11 – Tool for the study of Energetics and Dynamics of Protein
- Coot 0.7 / WinCoot 0.7.0.1 – Macromolecular Model Building Tool
- MODELLER 9.11 – Comparative Protein Structure Modeling
- ProtMod – Protein Modeling Server
- Swiss-PdbViewer 4.1 – Analyze Several Proteins 3D Structure at the Same Time
- SEQMOL 3.4.7 – Sequence Alignment & PDB Structure Analysis Utility
- GraphiteLifeExplorer 20120731 – Model in 3D Assemblies of Proteins and DNA
- DipoCoup 1.0 – 3D-structure Homology Comparison
- LigandScout 3.1b – Pharmacophore 3D Modeling
- MMV 2.5 – Visualization of Molecules
- Avogadro 1.1.0 – Molecule Editor & Visualizer
- BioViewer 1.5.7 – Read only version of BioEditor
- ModeHunter 1.2 – Normal Mode Analysis of Coarse Grained Elastic Networks
- Reduce 3.16 – Add Hydrogens to PDB Molecular Structure File
- SRS3D 1.4 – System for Displaying 3D Structures integrated with Sequences and Features
- Spanner 1.2.8 – Hybrid-template Structural Modeling
- COMBOSA3D 1.1 – Coloring Of Molecules Based On Sequence Alignment
- Reconstruct 1.0 – Reconstructing 3D Structures from Contact Maps
- MetalloPred – Hierarchical Prediction of Metal Ion Binding proteins
- Q-SiteFinder – Ligand Binding Site Prediction
- Uncoupler – Analysis of Coupled Folding and Binding
- CooperativeDimer – Analysis of Ligand Binding to Dimers
- Provar 4.81 – Probabalistic Analysis of Pocket Variation
- MDWeb / MDMoby – Web-based Platform for Molecular Dynamics Simulations
- Pentacle 1.0.6 – Advanced Alignment-Independent 3D QSAR
- Al-Eigen – Contact Map Overlap by Alignment of Eigenvectors
- FT-COMAR – Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps
- K-Fold – Predictor of the Protein Folding Mechanism and Rate
- PyRy3D 1.0.0 – Modeling of large Macromolecular Complexes
- AMMP 2.0 – Molecular Mechanics, Dynamics and Modeling program
- FiPD – Filter for Proteins Docking
- ZDOCK 3.0.2 / M-ZDOCK – Protein Docking
- Wordom 0.22 – Analysis of Molecular Dynamics Simulations
- SVMcon 1.0 – Protein Contact Map Prediction using Support Vector Machine
- FastContact 2.0 – Energy Scoring tool for Protein-protein Complex Structures
- PINTS – Patterns In Non-homologous Tertiary Structures
- MESHI 5.37 – Protein Modeling
- PAR-3D 1.1 – Detect Protein Active site Residues using 3-Dimensional Structural Motifs
- FoldX 3.0 beta3 – Force Field for Energy Calculations and Protein Design
- urms – Structure Comparison Algorithm
- ProSMoS – Protein Structure Motif Search
- VASCo 1.0.2 – Computation and Visualization of Annotated Protein Surface Contacts
- CADD 0.1.1 – Computer Aided Drug Discovery
- ePMV 0.5 – embedded Python Molecular Viewer
- NAMD 2.9 – Molecular Dynamics Program
- ARP/wARP 7.3 – Crystallographic Macromolecular Model Building
- PDBpaint 20111209 – Tag Protein Structures with Sequence Annotations
- RAPTOR 4.5 – Protein Structure Modeling
- Cadnano 2.2.0 – Design Three-dimensional DNA Origami Nanostructures
- MOSFLM 7.0.9 / iMOSFLM 1.0.7 – Integration of Macromolecular Diffraction Data
- ccp4 6.3.0 – Macromolecular X-Ray Crystallography
- SHIFTX2 1.07 – Improved Protein Chemical Shift Prediction
- Raster3D 3.0-2 – Generate High Quality Raster Images of Proteins or other Molecules
- g_correlation 1.02 – Generalized Correlation for Biomolecular Dynamics
- Solvate 1.0 – Construct Atomic Solvent Environment Model for Given Atomic Macromolecule Model
- EGO VIII – Molecular Dynamics Simulation
- g_permute 1.12 – Permutation-Reduced Phase Space Density Compaction
- FEATURE 3.0 – Examine Biological Structures
- Mol2Mol 5.6.3 – Molecule File Manipulation & Conversion
- KiNG 2.21 – Three Dimensional Vector Graphics
- DS Visualizer 3.5 & ActiveX Control 3.5 – Molecular Visualization
- XCrySDen 1.5.53 – Crystalline & Molecular Structure Visualisation
- ProteinGlimpse 1.6 – Visualize Macromolecules Retrieved from PDB
- Biskit 2.4.0 – Python Platform for Structural Bioinformatics
- Ghemical 3.0.0 – Molecular Modeling and Editing Package for GNOME
- ArgusLab 4.0.1 – Molecular Modeling, Graphics & Drug Design Program
- Hollow 1.2 – Illustration software for Proteins
- MoluCAD 1.034 – Molecular Modeling & Visualization Tool
- ModeRNA 1.7.1 – Comparative RNA 3D Modeling
- APBS 1.4.0 – Evaluat Electrostatic Properties of Nanoscale Biomolecular System
- AMBER 12 – Assisted Model Building with Energy Refinement
- RIP 1.1 – Accelerated Molecular Dynamics
- Probe 2.13 – Evaluate Atomic Packing & Contact Analysis
- MolPOV 2.1.0 – PDB to POV File Converter & Visualizer
- SODOCK – Swarm Optimization for Flexible Protein-Ligand Docking
- Ramachandran – Java Program For Drawing Ramachandran Plots
- PRNA – Prediction of protein-RNA binding sites
- PIPSA 3.0 – Protein Interaction Property Similarity Analysis
- TRITON 4.0 – Computational Aided Protein Engineering.
- POPS* 1.5.3 – Fast and Accurate Computation of Surface Areas of Proteins and Nucleic Acids
- GRAMM 1.03 / GRAMM-X – Protein-Protein Docking and Protein-Ligand Docking
- MDLab – Molecular Dynamics Simulation Prototyping Environment
- CompuCell3D 3.6.2 – 3D Multiscale Multi-cell Simulations
- FlexDock – Docking Algorithm for Automatic prediction of protein interactions with large scale motion.
- PepCrawler – Refinement and binding-affinity estimation of peptide inhibitors
- SymmRef – Refinement and re-ranking of symmetric docking solutions
- FiberDock – Flexible Induced-fit Backbone Refinement in Molecular Docking
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