Posts
- Category: 3D molecular model
- 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
- 3D-XCI - Inferring Three-dimensional Structures of the X-chromosome during X-inactivation
- 3DBIONOTES- WS - Interactive View of Macromolecular Information
- 3DChrom - Reconstruct Chromosome 3D Structures using Multidimensional Scaling
- 3DIANA - A Toolbox for Quaternary Structure Modeling
- 3DLigandSite - Ligand Binding Site Prediction Server
- 3Dmol.js 1.6.4 - Molecular Visualization with WebGL
- 3DNA v2.4.5 - Vsualization of Three-Dimensional Nucleic Acid Structures
- 3V 1.3 - Volume Related Calculations
- ABS-Scan - Webserver for Insilico Binding site Alanine Scanning Mutagenesis
- ActiveICM 1.2-4 - PowerPoint & Web Browsers Plugin to Display 3D Modules
- Adepth - Measures of Atomic Depths in Macromolecules
- ADP_EM 2.1 - 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
- AlloSigMA 2 - Allosteric Signalling and Mutation Analysis
- AlphaMol 1.0 - Tools for Biomolecular Geometry
- AMBER 20 - Assisted Model Building with Energy Refinement
- AmberTools 20 - Molecular Dynamics Simulation
- AMMOS 2 - 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 3.0.0 - 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 8.0 - Crystallographic Macromolecular Model Building
- Ascalaph 1.8.94 - Molecular Modelling Suite
- Athena - Molecular visualisation software for Solaris
- Atomdroid 1.5.0 - Molecular Viewer/Builder for Android
- ATSAS 3.0.3 - 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 4.0.3 - Use AutoDock Vina in Protein Inhibitor Design
- Avogadro2 1.90 - Molecule Editor & Visualizer
- AVP 1.3 - Calculate Protein Void Volumes and Packing Quality
- AxPyMOL 2.5 - PowerPoint Plug-In for Embedding 3D Molecular Images & Animations
- BALBES 1.1.5 - Molecular Replacement
- ballaxy - Galaxy-based workflow toolkit for Structural Bioinformatics
- Balloon 1.6.9 - Creates 3D Atomic Coordinates from Molecular Connectivity
- BALLView / BALL 1.5.0 - 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
- 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 2.0 - Analyzing Ligand Binding
- BindML/BindML+ - Detecting Protein-Protein Interaction Interface Propensity
- Bio3D v2.3 / Bio3D-web - Biological Structure Analysis
- BioBlender 1.0 - Software built on the Open-source 3D Modeling software Blender
- Biobox - Toolbox for Biomolecular Modelling
- Bioclipse 2.6.2 - Life Sciences Workbench
- Biodesigner 0.75 - Molecular Modeling & Visualization
- BIOVIA Discovery Studio Visualizer 4.5 - Molecular Visualization
- BioViewer 1.5.7 - Read only version of BioEditor
- Biskit 2.4.0 - Python Platform for Structural Bioinformatics
- BlendMol 1.3 - Advanced Macromolecular Visualization in Blender
- 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
- bSiteFinder - Protein-binding Sites Prediction Server
- BSP-SLIM - Low-Resolution Docking on Predicted Structures
- buccaneer 1.5 - Electron Density Interpretation/Protein Model Building software
- C2A 1.0 - Coarse to Atomic
- 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 1.1662 - Evaluation of Protein Structural Models against the Reference Structure
- Cadnano 2.5 - Design Three-dimensional DNA Origami Nanostructures
- CafeMol 3.2.1 - Biomolecular Modeling and Simulation Software
- CAVER 3.02 / CAVER Analyst 2.0 - software tool for Protein Analysis and Visualization
- CaverDock 1.01 - Analysis of Transport Processes in proteins
- CCBuilder 2.0.4 - Coiled-coil Protein Assemblies
- CCharPPI - Computational Characterisation of Protein-Protein Interactions
- CCOMP 3.70 - Compare Ligand/Receptor Complexes
- ccp4 v7.1.015 - Macromolecular X-Ray Crystallography
- CCP4mg 2.10.11 - Create Publication Quality Molecular Images and Movies
- ccPDB 2.0 - Compilation and Creation of datasets from PDB
- CH3Shift - Structure Based Prediction of Protein Methyl Group Chemical Shifts
- CHARMM 46 / CHARMM-GUI 3.6 - Macromolecular Dynamics and Mechanics / GUI
- ChemCraft b595b - 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
- 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
- CoCoPRED 20210818 - Coiled-coil Protein Structural Feature Prediction
- CombDock - COMBinatorial Asembly by mutiple DOCKing
- COMMA - Dissect Proteins Dynamical Architectures
- COMPLIG - Ligand Molecule Superposition tool
- COMPPDB - PDB Superposition Tool
- CompuCell3D 4.2.5 - 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
- ConSole - Contact Map based Solenoid Detection
- CONSRANK - Analysis,Comparison and Ranking of Docking Models based on Inter-residue Contacts
- CooperativeDimer - Analysis of Ligand Binding to Dimers
- Coot 0.9.6 / WinCoot 0.9.6 - Macromolecular Model Building Tool
- COSMOS 5.0 / COSMOS Viewer 3.0 - Computer Simulation & Visualisation of Molecular Structures
- CPORT - Prediction of Protein-protein Interface Residues
- CRDOCK - Dock Ligands in Macromolecules
- CreateFibril 2.5 - Build Atomic Resolution Models of Protein Fibrils
- CryoBayes beta - Bayesian method for Inferring 3D structure of Macromolecules
- CryptoSite - Predicting Cryptic Binding Site
- CrystalDock 1.0.0 - Molecular Design and Optimization
- CrystalMaker 10.6 - Build Crystal & Molecular Structures
- CS23D 2.0 - Protein Structure generation using NMR Chemical Shifts and Sequence data
- CSM-AB / mCSM-AB / mCSM-AB2 / mmCSM-AB- Predicting Antibody-antigen Binding Affinity
- CSM-lig / mCSM-lig - A Web Server for Assessing and Comparing Protein-small molecule Affinities
- CueMol 2.2.3.443 - Macromolecular Structure Visualization
- CyToStruct 0.2.5.2 - Launching Arbitrary External Apps (such as Viewers) for Nodes/Edges
- Dang 1.8 - Read PDB File & Generate Geometric Measurement Table
- Dangle 0.63 - Read PDB File & Generate Geometric Measurement Table
- DBPnet v0.1.4 - Inferring cooperation of DNA Binding Proteins in 3D genome
- Desmond 2.4 - High-speed Molecular Dynamics Simulation
- DINO 0.9.5 - Structural Biology Data 3D Visualization
- DipoCoup 1.0 - 3D-structure Homology Comparison
- DireX 0.71 - Low-resolution Structure Refinement
- Disulfide by Design 2.12 - Disulfide Engineering in Proteins
- DL_POLY 4 v5.0.0 - Molecular Dynamics Simulations
- do_x3dna 2018 - Analyze Fluctuations in DNA or RNA Structures in Molecular Dynamics Trajectories
- DOCK 6.9 - Docking Molecules to each other
- DockAFM - Docking Structures under an AFM surface
- DockingApp / DockingApp RF - Application for Docking and Virtual Screening
- DOCKSCORE - Ranking Protein-protein Docked Poses
- DockStar - Modelling of multimolecular Protein Complexes
- DoGSiteScorer 2.0 - Binding Site Prediction, analysis and Druggability Assessment
- Dove - A Deep-learning based dOcking decoy eValuation mEthod
- DPS 2.13 - Processing of Single Crystal X-ray Diffraction data of proteins etc
- Dynamical Network Analysis - Characterizing Allosteric Signalling through Biomolecular Complexes
- DynDom 1.5 / DynDom3D 1.04 - Protein Domain Motion Analysis
- eAromatic - Analysis of Aromatic Interactions in Protein-ligand Complexes
- eBoxSize 1.1 - Calculating an optimal box size for Ligand Docking and Virtual Screening
- EdaFoldAA / EdaFold 0.1 - Protein Structure Prediction
- EDTSurf - Quick and Accurate Construction of Macromolecular Surfaces
- eFindSitePPI - Detect Protein Binding Sites and Residues with Meta-threading
- EGO VIII - Molecular Dynamics Simulation
- EleKit 2 - Electrostatic Similarities between Protein and Small Molecule Ligands
- Elves 1.3.6.1.2 - Conversational User Interface to the most common X-ray Crystallography programs
- eMatchSite 1.0 - Sequence Order-independent Ligand Binding Site Alignment
- eMovie 1.04 - Make Molecular Movies
- EpiTensor 0.9 - Constructing 3-D interactions from 1-D Epigenomes
- epitope3D - Machine Learning method for conformational B-cell Epitope prediction
- ePMV 0.5 - embedded Python Molecular Viewer
- EPOS_BP 1.0 - Ensemble of Pockets on Protein Surfaces with BALLPass
- EPPIC 3.3.3 - Evolutionary Protein-Protein Interface Classifier
- eSBMTools 1.04 - Python tools for enhanced Native Structure-based Modeling
- ESmol 0.74 / NDKmol 0.97 - Molecular Viewer for Android
- Facio 23.1.3 - 3D-Graphics program for Molecular Modeling and Visualization
- FALC-Loop - Protein Loop Modeling Server
- FALCON@home - High-throughput Protein Structure Prediction server
- FastContact 2.0 - Energy Scoring tool for Protein-protein Complex Structures
- FEATURE 3.1 - Examine Biological Structures
- FG-MD - High-resolution Proteins Structure Refinement by Fragment-Guided MD simulation
- FiberDock - Flexible Induced-fit Backbone Refinement in Molecular Docking
- FiltRest3D - Filtering Protein Models by Fuzzy Restraints
- FINDSITE 1.0 - Ligand-binding Site Prediction & Functional Annotation
- FireDock - Fast Interaction REfinement in molecular DOCKing
- Fit3D v005 - Small Structural Motif Screening in Proteins and further analyses
- Flex-EM - Fitting and Refinement of Atomic Structures
- FlexAID 2.48 / NRGsuite 2.48f - Revisiting Docking on Non-Native-Complex Structures
- FlexDock - Docking Algorithm for Automatic prediction of protein interactions with large scale motion.
- FlexPred - Protein Fluctuation Prediction using SVR
- FlexS 2.1.3 - Predict Ligand Superpositions
- Flipkin 2.4 - Script to Make the Kinemages
- FMA 0901 - Protein Functional Mode Analysis
- FOLD-EM - Fully Automated Fold Recognition in Electron Density Maps
- FoldHandedness - The determination of the handedness of α-helices
- FoldHSphere - Deep Hyperspherical Embeddings for Protein Fold Recognition
- FoldNucleus - Calculation the Folding Nucleus for RNA or Protein
- FoldX 3.0 - Force Field for Energy Calculations and Protein Design
- FragHMMent 1.24 - Residue-residue Contact Prediction
- FRETraj v0.2.6 - Integrating Single-molecule Spectroscopy with Molecular Dynamics
- FRETsg 1.0 - Structure Building from Multiple FRET Distances
- Friend 2.0 - Multiple Structure Visualization & Multiple Sequence Alignment
- FRODOCK 3.12 - Fast Rotational DOCKing tool
- FT-COMAR - Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps
- FTDock 2.0/ RPScore /MultiDock 1.0 - Protein Molecule 3D-Dock Suite
- FTProd - Binding Site Comparison across Multiple Structures
- FuncPatch - Inferring Conserved Functional Regions in Protein Tertiary Structures
- FunFOLD 3.0 - Protein-Ligand Binding Site Prediction Server
- g_correlation 1.02 - Generalized Correlation for Biomolecular Dynamics
- g_permute 1.12 - Permutation-Reduced Phase Space Density Compaction
- Gabedit 2.4.8 - Graphical User Interface to Computational Chemistry Packages
- GalaxyDock 2 - Protein-ligand Docking program
- GAP 1.2.14 - Geometric Analysis of Proteins
- Garlic 1.6 - Free Molecular Viewer and Editor
- GeauxDock v2 - GPU Accelerated Molecular Docking
- Gen3D - 3D Genome and Chromosome Structural Model Construction
- GeNMR - Webserver for Protein Structure generation from NOE Distant Restraints and Chemical Shifts
- Geno3D r2 - Protein Molecular Modelling
- Ghemical 3.0.0 - Molecular Modeling and Editing Package for GNOME
- GIANT - Pattern analysis of Molecular Interactions in 3D Structures of Protein–small Ligand Complexes
- GLmol 0.47 - Molecular Viewer on WebGL/Javascript
- GLoSA 2.2 - Protein-ligand and Protein-protein Interactions
- GMOL 2 - 3D Genome Structure Visualization
- GMQ - Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors
- GOAP - Protein Structure Prediction
- GOdMD - Conformational Transitions with discrete Molecular Dynamics
- Gorgon 2.2.0 - Molecular Modeling system
- GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures
- GPCR-ModSim - Computational Modeling and Simulation of G-Protein Coupled Receptors
- GPCRautomodel - Automatic Modeling of Mammalian Olfactory Receptors and Docking of Odorants
- GPGPUFRAGFOLD 0.1 - CUDA Fragment Assembly Based Protein Structure Prediction
- GRAMM 1.03 / GRAMM-X - Protein-Protein Docking and Protein-Ligand Docking
- GraphiteLifeExplorer 20120731 - Model in 3D Assemblies of Proteins and DNA
- GRASP 2 -Visualization of Macromolecular Structures and Sequences
- GRE4Zn - Geometric REstriction for Zinc-binding
- GROMACS 2019.4 - Molecular Simulation
- Gromita 4.6 - GUI for GROMACS
- GS-align - Glycan Structure Alignment and Similarity Measurement
- GSC 1.2 - NMR Chemical Shift Comparison
- GWOVina 1.0 - Fast Protein-ligand Docking tool based on GWO and AutoDock Vina
- HAAD - Quick and Accurate Hydrogen Atom Addition
- HADDOCK 2.2 - Docking approach for the Modeling of Biomolecular Complexes
- HaptiMOL ISAS 3.0 / HaptiMOL ENM 1.1 - Interact with Molecules via Haptic Feedback Devices.
- HDOCK 1.1 - Protein-protein and Protein-DNA/RNA Docking based on Hybrid Strategy
- HiCNet - Reconstruct High-resolution Chromosome 3D Structures based on Hi-C Complex Networks
- HingeProt - Protein Hinge Prediction Using Elastic Network Models
- Hollow 1.3 - Illustration software for Proteins
- HotMAPS v1.1.4 - Hotspot Missense mutation Areas in Protein Structures
- HotSpot Wizard 3.0 - Identification of Hot Spots in Protein Engineering
- HPEPDOCK - Blind Peptide-protein Docking based on Hierarchical Algorithm
- i3Drefine / 3Drefine - Protein 3D Structure Refinement
- ICM-Browser 3.9-2b - Molecules & Sequence Alignments Visualization
- idock 2.2.3 - Structure-based Virtual Screening powered by fast and flexible Ligand Docking
- iGEMDOCK 2.1 - Recognizing Pharmacological Interactions and Virtual Screening
- iMOD 1.04 - Multipurpose Normal Mode Analysis in Internal Coordinates
- iMODFIT 1.51 - Fitting of Atomic Structures into EM maps based on iMOD
- iMol 0.40 - Molecular Visualization Application for Mac OS X
- iMolview 1.9.5 - iPhone, iPad and Android App for Browsing Protein, DNA & Drug Molecules in 3D
- IMP 2.15.0 - Integrative Modeling Platform
- InfMod3DGen - Inferential Modeling of 3D Chromatin Structure
- InteractiveROSETTA 2.3.0 - GUI for PyRosetta Protein Modeling Suite
- InterKnowlogy 3D Molecule Viewer 20080324
- intf_model - Protein-DNA Modeling Interface
- IntFOLD 5.0 - Integrated Protein Structure and Function Prediction Server
- ION 2 - Calculates the Distribution of Ions around Biomolecules
- Ionize 1.6.0 - Placement Atomic Ions around 3D Biomolecular Structure
- IRECS 1.3 - Predict Conformation of Protein Side Chains
- ISAMBARD v2.3.1 - Intelligent System for Analysis, Model Building And Rational Design of Biomolecules
- ISIM Interface 1.3.2 - Graphical Interface for running the program ISIM
- IsoMIF 20150311 - Detection of Molecular Interaction Field Similarities
- J3DPSV 1.0 - Java Three-dimensional (3D) Protein Structure Viewer
- JabberDock - Protein Docking using a density-based descriptor for Atoms Charge and Dynamics
- Jackal 1.5 - Protein Structure Modeling Package
- JADOPPT - Java based AutoDock Preparing and Processing Tool
- Jamberoo 11 - Cross-Platform Molecular Editor & Builder
- Jimp 2 0.091 - Visualize and Manipulate Molecules
- Jmol 14.31.44 - Java Viewer for Chemical Structures in 3D
- Jolecule 2.0 - HTML5 Web-based Three-Dimensional Protein and DNA Renderer
- jSim for Gromacs 0.63b - Graphical User Interface for Gromacs
- JyMOL 1.0 - Java-based Molecular Visualization
- K-Fold - Predictor of the Protein Folding Mechanism and Rate
- Kin2Dcont 1.8 & Kin3Dcont 1.12 - Produce Molecule Contour Map
- KiNG 2.21 - Three Dimensional Vector Graphics
- KinImmerse 0.5 - Translate Kinemage Files into Software for Virtual Environment
- KORP v1 - knowledge-based 6D potential for Protein and Loop Modeling
- KYG - RNA Interface Residue Prediction from Protein 3D Structure
- lDDT - Comparing Protein Structures and Models using Distance Difference Tests
- LIBRA v1 / LIBRA+ / LIBRAWA - Ligand Binding site Recognition Application
- LigAlign 1.0 - Ligand-based Active site Alignment and Analysis
- LigandScout 3.12 - Pharmacophore 3D Modeling
- LIGPLOT 4.5.3 / LIGPLOT+ 2.2 - Plot Schematic Diagrams of Protein-ligand Interactions
- LipidWrapper 1.15 - Lipid Bilayer Modeling
- LIQUID 1.0 - Pymol Plugin for Fuzzy Pharmacophore Models
- LJ3D - Inferring Single-Cell 3D Chromosomal Structures based on the Lennard-Jones potential
- LocalMove - Compute On-lattice Fits for Biopolymers
- LoopTK 2.0.1 - Protein Loop Kinematic Toolkit
- lrrr 1.4 beta1 - Determines Ligands on the Surface of Proteins
- LSim 1.0.0 - Superposes Macromolecular Electron Densities and Computes Structural Similarity Score
- LZerD / Multi-LZerD / PI-LZerD - (Multiple) Protein-Protein Docking Algorithm
- Mage 6.47 - Kinemage File 3D Display
- MAINMAST 1.0 - MAINchain Model trAcing using Spanning Tree from a EM map
- MAPOR 1.0 - MutAtion LandscaPe GeneratOR
- 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
- MASTER - Method of Accelerated Search for Tertiary Ensemble Representatives
- Mc-Sym 3.3.2 - Molecular Modeling using Constraint Satisfaction
- MCMC5C - Prediction of Chromatin 3D Structure
- MCQ4Structures 1.6.1 - Computing Similarity of 3D RNA / Protein Structures
- McQSAR 1.3.0.92 - Generate Quantitative Structure-activity Relationships
- MD Morphing 1.0 - Perform Molecular Dynamics Morphing Simulations
- MDLab - Molecular Dynamics Simulation Prototyping Environment
- MDWeb / MDMoby - Web-based Platform for Molecular Dynamics Simulations
- MDynaMix 5.2.8 - Molecular Dynamics Program
- MEGADOCK 4.1.1 / MEGADOCK-K 3.0 / MEGADOCK-GPU 1.0 - Protein-protein Interaction Prediction System
- MEMBPLUGIN 1.1RC2 - Studying Membrane Complexity in VMD
- MembraneEditor 2.2.2_2 - Modeling, Visualization and Analysis of PDB-based Membranes
- Memoir - Membrane Protein Modelling Pipeline
- MEPSA 1.4 - Minimum Energy Pathway Analysis for Energy Landscapes
- MERMAID - Prepare and Run Coarse-Grained Membrane Protein Dynamics
- MESHI 5.37 - Protein Modeling
- MetalloPred - Hierarchical Prediction of Metal Ion Binding proteins
- metaRNAmodules 1.0.2 - Automated RNA 3D Module Extraction and Modeling
- mfDCA - mean field Direct Coupling Analysis
- MGA-Glide 1.0 - Grid-based Protein-ligand Docking software
- MGLTools 1.5.6 - Visualization & Analysis of Molecular Structures
- MINT 3.2 - User Interface to Modeller
- MM-ISMSA - Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics
- mMaya 1.3 - Molecular Maya toolkit
- MMB 2.19 - Model the Structure and Dynamics of Macromolecules
- MMPRO 0.7 - Molecule Visualization & Analysis Program
- MMTK 2.7.9 - The Molecular Modelling Toolkit
- MMTSB toolset - Multiscale Modeling Tools for Structural Biology
- ModeHunter 1.2 - Normal Mode Analysis of Coarse Grained Elastic Networks
- MODELLER 10.1 - Comparative Protein Structure Modeling
- Models@Home 12.1 - Distributed Computing Software for Protein Modeling
- ModeRNA 1.7.1 - Comparative RNA 3D Modeling
- ModFOLD 6 - Model Quality Assessment Server
- ModPipe 2.3.0 - Calculate Protein Structure Model
- ModRefiner 20111024 - High-resolution Protein Structure Refinement
- ModView 0.903 - Visualization of Multiple Protein Sequences & Structures
- MOGEN 1.0 - 3D Genome Reconstruction
- MOIL 12.0.3923 - Molecular Modeling Software
- MOITF-EM - Automated Computational Tool for Identifying Conserved Domains in CryoEM Structures
- Mol2Mol 5.6.3 - Molecule File Manipulation & Conversion
- MOLA - System for Virtual Screening using AutoDock4/Vina on Computer Clusters
- MOLARIS-XG 9.15 - Tool for the study of Energetics and Dynamics of Protein
- MOLDEN 5.8.2 - Package for Displaying Molecular Density
- MOLE 2.5 - Location and Characterization of Channels, Tunnels and Pores in Molecular Structures
- Molecule 3D 3.9 - 3D Molecular Visualizator for Android
- Molecule Viewer 3D 1.2.5 - 3D Molecular Viewer for Android
- Molecule World DNA Binding Lab 1.1.1 / Molecule World 2.2.0 - Viewing Molecular and Chemical 3d Structures
- Molecules 2.1 - iPhone / iPad Application for PDB Structures
- Molekel 5.4.0 - 3D Molecular Visualization Program
- MolFit 2 - Protein-Protein docking Program
- MolPOV 2.1.0 - PDB to POV File Converter & Visualizer
- MolScript 2.1.2 - Display Molecular 3D Structures
- Molstack 1.3 - Platform for Sharing Electron Density Maps and their Interpretations
- MolSurfer 1.2 - a Macromolecular Interface Navigator
- MoluCAD 1.034 - Molecular Modeling & Visualization Tool
- MolView - Exploratory 3D Molecule Viewer
- MORPHEUS - Identify Residues in Predicted Models with a large Error
- MoSART pr - NMR-based Biomolecular Structure Computation
- MOSBY 0.955 - View Atomic Structures of Protein Molecules
- MOSFLM 7.4.0 / iMOSFLM 7.3.0 - Integration of Macromolecular Diffraction Data
- MotAn ver. beta.1603061903 - Motif Analyzer for Protein 3D Structures
- MovieMaker 1.0 - Rendering of Protein Motions and Interactions
- MPRDock - Protein-ensemble-RNA Docking by efficient Consideration of Protein Flexibility
- MrBUMP 0.4.4 - Automated Molecular Replacement
- MSMExplorer 0.9 - Visualization Application for Markov State Models for Folding
- MSPocket 1.1 - Detection and Graphical Analysis of Protein Surface Pockets
- MTMDAT-HADDOCK 201210 - High-throughput, Data-driven Protein Complex Structure Modelling
- MultiFit - Fitting of Multiple Proteins into their Assembly Density Map
- MVP/MVP-Fit 2.0 - Macromolecular Visualization and Processing
- myPresto 5.000 / omegagene 0.38 - Medicinally Yielding PRotein Engineering SimulaTOr
- NAContacts 2.5 - Write Contact Information between Nucleic Acid Bases
- NAFlex - Analysis of Nucleic Acids Flexibility
- NAMD 3.0 - Molecular Dynamics Program
- NAST 1.0 - Nucleic Acid Simulation Tool
- Nautilus 0.2 - Electron Density Interpretation/Nucleotide Model Building software
- NeEMO 1.0 - NEtwork Enthalpic MOdelling
- NGL Viewer 0.9.3 - Web Application for Molecular Visualization
- NIP_NSc - Dentify Compactness at Protein-protein Contacts
- NMFF - Normal Mode Flexible Fitting
- NMSim - Modeling Macromolecular Conformational Transitions
- NOC 3.01 - Molecular Explorer for Protein Structure Visualization
- NPDock - Nucleic acid-Protein Dock
- nuccyl 1.5.2 - Allows PyMOL to display Atomic Models of Nucleic Acids in High Representation
- NUCPLOT 1.1.4 - Generate Schematic Diagrams of Protein-nucleic Acid Interactions
- Numbat 0.99 - Automatic Δχ-tensor Determination
- OB Score 1.0 - Structural Genomics Target Ranking
- Omokage search - Shape Similarity Search of Macromolecules
- OpenAstexViewer 3.0 - Software for Molecular Visualisation
- OpenGrowth 1.0.1 - Construct de novo Ligands for Protein
- OpenMM 7.4 / PyOpenMM 4.0 - Library for Molecular Modeling Simulation
- OpenMM Zephyr 2.0.3 - Molecular Simulation Application
- OpenStructure 2.2 - Computational Structural Biology Framework
- Orb 1.2 / orbplus 1.1.2 - Chemical Shift Prediction
- ORTEP-III 1.03 /for Windows 2021.3 - Crystal Structure Illustration
- Oscail 2021 - Crystallography & Molecular Modelling
- OWL v2.2.0 - Java toolkit for Computational Structural Biology
- P2Rank 2.0.1 - Protein-Ligand Binding Site prediction
- p3d 0.4.3 – Python module for Structural Bioinformatics
- PaDEL-ADV 1.6 - Facilitate Virtual Screening with AutoDock Vina
- PALES - Prediction of ALignmEnt from Structure
- PANTHER - Novel tool to Predict Small Molecule Binding into Proteins
- PARS - Protein Allosteric and Regulatory Sites
- PASTIS 0.3.3 - Poisson-based Algorithm for STable Inference of DNA Structure
- PatchDock Beta 1.3 - Rigid Unbound Docking of Molecules
- PatternQuery 1.1.17.5.30 - Find Atom Patterns in Molecular Databases
- PCAViz 1.2 - Visualizing Molecular Dynamics Simulations in the Web Browser
- PDB Editor 090203 - PDB (Protein Data Bank) File Editor
- pdb_extract 3.11 - Prepare Data for Submission to the PDB
- PDB-Explorer - Web-based interactive Map of PDB in Shape Space
- pdb-tools 0.2.1 - Editing and Performing Calculations on wwPDB Files
- PDBCNS 2.0 - Interconvert Atom Names between PDB & CNS formats
- PDBest 1.40 - Manipulating and Enhancing Protein Structures
- PDBFlex - Exploring Flexibility in Protein Structures
- PDBHighlight 1.1.0 - A RasMol Script database
- PDBjViewer 4.5.5 - Display 3D Molecular Graphics of Proteins and Nucleic Acids
- PDBlib 2.2 - C++ Macromolecular Class Library
- PDBpaint 20111209 - Tag Protein Structures with Sequence Annotations
- PDBpy - Python Parser for PDB files
- PDC 2 - Calculate Effective Charges for Macromolecules
- PDIviz 1.2.3 - Visualization of Protein-DNA Binding Interfaces
- Pentacle 1.0.7 - Advanced Alignment-Independent 3D QSAR
- PepBDB - An Information Portal to Biological Peptide-protein complex structures
- PepCrawler - Refinement and binding-affinity estimation of peptide inhibitors
- PeptideBuilder 1.0.4 - Python Library to Generate Model Peptides
- PGC 1.0b - Protein Geometry Calculator
- Phaistos 1.0 - Proteins Structure Prediction
- PHENIX 1.19.2 - Python-based Hierarchical ENvironment for Integrated Xtallography
- Phyre 2.0 - Protein Homology/analogY Recognition Engine
- PIBASE v2010 - Database of structurally defined Protein Interfaces
- PINTS - Patterns In Non-homologous Tertiary Structures
- PIPSA 4.0.2 / multiPIPSA - Protein Interaction Property Similarity Analysis
- PLATINUM - Protein–Ligand ATtractions Investigation NUMerically
- pmx - Python Library and Tools for Computational and Structural Biophysics
- PNImodeler - Protein-Nucleic Acid Interaction Modeler
- PocketAnalyzerPCA 1.30 - Pocket-space Maps to Identify novel Binding-site Conformations in Proteins
- PONDEROSA-C/S 20181026 - Automated Protein 3D structure Determination
- PONDEROSA-CS 2018 - Determine Protein 3D Structures
- PovChem 2.1.1 - Chemical Visualization & Illustration & POV File Converter
- povme 2.2.1 - Measuring Binding-pocket Volumes
- PowerFit 2.0.0 - Rigid body fitting of Atomic Strucures in Cryo-electron Microscopy Density Maps
- PPDbench - Benchmarking of Docking software on Protein-peptide Complexes
- Prediction of Protein-DNA Interactions based on Alpha Shape Modeling
- Prekin 6.51 - Prepares Kinemages Files from PDB-format Files
- PREPI 0.9 - Molecular 3D Representation
- PrinCCes 1.09 - Protein Internal Channel & Cavity Estimation
- PRISM 2.0 - Prediction of Protein-protein Interactions and Modeling their 3D Complexes
- PRNA - Prediction of protein-RNA binding sites
- Probe 2.16 - Evaluate Atomic Packing & Contact Analysis
- ProbeWithO 0.9.0 - Use Small Probe Contact Dots Within O
- ProBiS 2.4.2 - Protein Binding Sites Detection
- PRODIGY 2.0 - Predicting the Binding Affinity of Protein-protein Complexes
- ProDy 1.10.10 - Python package for Analysis and Modeling of Protein Structural Dynamics
- ProFit 3.1 - Protein Least Squares Fitting
- ProKware 0.95 - Present Protein Structural Properties in Protein Tertiary Structures
- ProNOI - Protein Nano-Object Integrator
- PROPORES - PROtein PORE Identification ToolS
- ProSa 2003 - Protein Structure Research Tool
- ProSMoS - Protein Structure Motif Search
- ProSTRIP - Find Similar Structural Repeats in Three-dimensional Protein Structures
- PROTARCH - Predict Protein Structure
- PROTEAND 1.0 - Display Macromolecular Structural Uncertainty
- Protein Explorer 2.80 - Visualize 3D Structures of Macromolecules
- ProteinScope 1.0.5 - 3D Protein Structure Viewer
- ProteinShader beta 0.9.4 - Illustrative Rendering of Macromolecules
- ProteinVis - Protein Visualization Program
- ProteinVR 1.0.7 - Browser-based, virtual-reality visualization of Molecular Structures
- ProtMod - Protein Modeling Server
- ProtoMol 3.3 - Molecular Dynamics (MD) Simulation
- ProtOn 1603061903 - Description of Protein 3D structure in terms of Architecture, Topology and Motifs
- ProtPOS 1.1 - Fast Prediction of Protein Preferred Orientation on a Surface
- ProTSAV 1.0 - Protein Tertiary Structure Analysis and Validation server
- Provar 4.81 - Probabalistic Analysis of Pocket Variation
- PSOVina 2.0 - Fast Protein-ligand Docking tool based on PSO and AutoDock Vina
- PSpacE Beta - Protein Structure Space Explorer
- PSTP-finder 0.4.3.1 - Protein Surface Transient Pocket Finder
- PULCHRA 3.04 - All-atom Reconstruction & Refinement of Reduced Protein Models
- PyDeT - PyMOL Plug-in for Visualizing Geometric Concepts around Proteins
- pyDockSAXS - Protein-protein Interactions using SAXS and Computational Docking
- pyDockWEB - Rigid-body docking and scoring by pyDock
- PyInteraph 1.0 - Analysis of Interaction Networks in Structural Ensembles of Proteins
- PyMOL 2.5.0 - Molecular Visualization System
- PyOpenMM 3.0 - Python API of OpenMM Library
- PyPDB 2.0 - a Python API for the Protein Data Bank
- PyPLIF 0.1.1 - Python-based Protein-Ligand Interaction Fingerprinting
- PyRx 0.9.8 - Virtual Screening software for Computer-Aided Drug Design
- PyRy3D 4.2.0 - Modeling of large Macromolecular Complexes
- PyWATER 1.0 - Find Conserved Water Molecules in Proteins by clustering
- QMEAN - Server for Model Quality Estimation
- QMol 4.0.2 - Visualizing Protein Structures
- QTree 2.3 - Graphics Rendering using Quad-tree Algorithm
- QUARK - De Novo Protein Structure Prediction
- QuickLookPDB - QuickLook plugin for Displaying PDB Files
- QuickPDB 20021101 - Java Applet for quickly viewing PROTEIN PDB Structure
- QuteMol 0.41 - Molecular Visualization System
- R3D Align - RNA 3D Structure Alignment
- R3D-2-MSA - RNA 3D Structure-to-Multiple Sequence Alignment Server
- Ramachandran Plot Explorer 1.0 - Interactive Cross-platform Protein Viewer
- RaptorX / RaptorX-SS8 - Protein Structure Prediction Server
- RaptorX Property 1.02 - Protein Structure Property Prediction
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