Molecular Modeling Software
@biosoftcn avidly tweets and curates bioinformatics and modeling software (collected at http://www.mybiosoftware.com). We selected some links relevant to you molecular modelers. Feel free to add software not found here through the comments.
- 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
Protein analysis:
- 3MATRIX 1.0 – Motif in 3D
- 3MOTIF 2.0 – Motif in 3D
- Alphabet – Find Groups of Amino Acids that Co-occur in Columns Frequently
- Anchor – Predict Binding Regions in Proteins
- annot8r_physprop 0.1 – Predict Physical Properties of Peptides
- ANTHEPROT 6.0 – Protein Sequence Analysis
- APAT 1.4.1 – Automated Protein Annotation Tool
- APEX 1.1.0 – Quantitative Proteomics Tool
- assp 1.2 – Assess Protein Secondary Structure Prediction Accuracy
- BepiPred 1.0b – Linear B-cell epitopes
- BSpred – Predict Binding Site of Proteins
- CDPred 1.01 – Conserved Domain-based Prediction
- ChloroP 1.1 – Predict Chloroplast Transit Peptides
- CLANS 20101007 – Visualize Protein Families based on Pairwise Similarity
- CLC Protein Workbench 5.5.2 – Workbench for Protein Analysis
- CoBaltDB 1.0 – Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database
- ConTest 1.0.1 – Test Constraints in Proteins
- CRC64 2006 – Improved 64-bit Cyclic Redundancy Check for Protein Sequences
- CS-PSeq-Gen 1.0 – Simulation of Protein Sequences under Constraints
- DASher 1.3.4 – Protein Sequence Client for DAS
- dasty 3.0.0.8 – Visualize Protein Sequence Feature Information using DAS
- DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein
- DICROPROT 2000 – DICHROism of PROTeins
- DISCO 1.0 – Structure Determination of Protein Homo-oligomers
- DiscoTope 1.1a – Predicts Discontinuous B cell Epitope
- Discriminative HMMs – Find Discriminative Motif to Predict Protein Subcellular Localization
- DisEMBL 1.5 – Protein Disorder Prediction
- DISOPRED 2.43 – Intrinsic Protein Disorder Prediction
- DomainFinder 2.0.4 – Determine Dynamical Domains in Protein
- eBLOCKS – Database of Conserved Protein Regions
- EFICAz2 1.3 – Accurate Sequence based Approach to Enzyme Function Inference
- eSIGNAL 1.0 – Database of Medline MeSh Terms & Protein Motifs that Detect Signal Transduction Proteins
- estzmate – Assess Potential for Protein Coding Region
- FFAS 03 – Pretein Structure Prediction based on Profile-profile Comparison
- Folding@home 6.23 – Understand Protein Folding, Misfolding & Related Diseases
- FoldMiner 200312 – Structural Similarity Searches and Motif Discovery
- GPMAW 9.10 – Mass Spectrometric Analysis of Proteins and Peptides
- greylag 0.2.2 – Tandem Mass Spectrum Peptide Identification and Validation
- HBAT 1.1 – Hydrogen Bond Analysis Tool
- HMMER 3.0 – Protein Sequence Homology Search
- HMMSTR 20091212 – Protein Secondary Structure Prediction
- HMMSTR-CM – Protein Contact Map Prediction
- HMMSUM – Structure-based Substitution Matrices
- HMMTOP 2.9 – Predict Transmembrane Helices and Topology of Proteins
- Hydrophobicity – Display Hydropathic Character of Protein
- I-sites 2 – Predict the Local Structure of a Protein
- I-TASSER 1.1 – Protein Structure & Function Predictions
- InteroPorc 2.0.2 – Automatic Molecular Interaction Predictions
- InterProScan 5 – Protein Domains Identifier
- InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks
- IUPred – Predict Intrinsically Unstructured Regions of proteins
- Jali 1.3 – Remote Homology Detection for Protein
- Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment
- LipoP 1.0a – Prediction of Lipoproteins & Signal Peptides in Gram Negative Bacteria
- MASKER – Molecular Surface Area Calculator
- MDT 5.1 – Prepares a raw Frequency Table
- MEME 4.7.0 – Discovering Motifs within the Sequences
- MEMPACK – SVM Prediction of Membrane Helix Packing
- MEMSAT 3 – Transmembrane Protein Structure Prediction
- MEMSAT-SVM – SVM Transmembrane Protein Structure Prediction
- MetaTM 1.1 – Predicte Transmembrane Topology
- mkdom/Xdom 2 – Build the ProDom Database
- MODELESTIMATOR 1.1 – Estimate Amino Acid Replacement Rates
- MPEx 3.2 – Tool for Exploring Membrane Proteins
- MPtopoQuerier – Search Database of Membrane Proteins
- MultiLoc2 20091026 – Predict Animal, Plant and Fungal Protein Subcellular Localization
- NAP – Nucleotide Amino Acid Alignment
- NASCA 20110516 – Side-chain Resonance Assignment & NOE Assignment
- NetCGlyc 1.0c – Predict C-mannosylation
- NetChop 3.1b – Neural Network Predictions for Cleavage Sites of Human Proteasome
- NetCTL 1.2a – Predict CTL Epitopes in Protein Sequence
- NetMHC 3.0c – predict Binding of Peptides to MHC Class I Alleles
- NetMHCII 2.2 – Predict Binding of Peptides to MHC class II Alleles
- NetMHCIIpan 2.0a – predict Pan-specific Binding of Peptides to MHC class II HLA-DR Alleles
- NetMHCpan 2.4 – Predicts Binding of Peptides to Known MHC Molecule
- NetNGlyc 1.0a – N-linked glycosylation sites in human proteins
- NetOGlyc 3.1d – Predict Mucin-type O-glycosylation
- NetPhos 3.1 – Generic Phosphorylation Sites in Eukaryotic Proteins
- NetSurfP 1.0 – Protein Surface Accessibility & Secondary Structure Predictions
- NOXclass – Prediction of Protein-protein Interaction Types
- NQ-Flipper 2.7 – Validate Asparagine and Glutamine Side-chain Amide Rotamers in Protein Structures
- NRPSpredictor2 20110911 – Predict NRPS Adenylation Domain Specificity
- NucImport – Nuclear Protein Import and Localisation Signals Predictor
- NucPred 1.1 – Predicting Nuclear Localization of Proteins
- OSPREY 1.0 – Computational Structure-based Protein Design
- Osprey 1.2.0 – Protein-protein Interaction Networks Visualization System
- PairwiseStatSig 20081215 – Pairwise Statistical Significance
- PexSPAM 1.2 – Protein Sequence Feature Extraction
- pfilt – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions
- pGenTHREADER 8.7 – Protein Fold Recognition by Profile-profile Threading
- Phobius /PolyPhobius 1.05 – Combined Transmembrane Topology & Signal Peptide Predictor
- PISCES 1.0 – Protein Sequence Culling Server
- PIVOT 2.0 – Protein Interactions VisualizatiOn Tool
- PoSSuM / PoSSuMsearch 2.0 – Matching of PPSSMs using Enhanced Suffix Arrays
- Pratt 2.1 – Find Flexible Patterns in Unaligned Protein Sequences
- ProBias/BIAS – Detect Compositional Bias in Biological Sequences
- ProCon 1.1 – Localization & Visualization of Protein Conservation
- ProCope 1.2 – Protein Complex Prediction and Evaluation
- ProP 1.0c – Arginine & Lysine propeptide Cleavage Sites in Eukaryotic Protein
- ProQ 1.2 – Protein Quality Predictor
- ProTag 1.4 – Office Add-In for offering SmartTag of Protein
- PROTEAN – Torsion Space Molecular Simulations
- Protein Coverage Summarizer 1.3.4053 – Determine Percent of Residues in Protein Sequence
- ProteinVis 2.1.6 – Tree viewer for Hierarchical Clusterings of Proteins
- ProteoWizard 2.0 – Proteomics Data Analysis
- PROTMAP2D 1.2.2 – Calculation, Visualization & Comparison of Contact Map
- PSAAM – Protein Sequence Analysis And Modelling
- PSI Protein Classifier 1.0.1.49 – Automation of the PSI-BLAST Results Analysis
- PSIPRED 3.21 – Accurate Protein Secondary Structure Prediction
- PSORTb 3.0.3 – High-precision Localization Prediction for Bacterial Proteins
- PSSpred 1.0 – Multiple Neural Network Training program for Protein Secondary Strucure Prediction
- ps_scan 1.75 – PROSITE scanning program
- PyRosetta 2.0 – Python-based Interface to Rosetta Molecular Modeling Suite
- RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination
- REPRO – Protein Repeats Analysis
- Rosetta 3.3 – Simulation and Design of Protein
- RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition
- SAPTF 1.7 – Sequence Analysis Plugin Tool Framework
- SCANPS 2.3.11 – Protein Sequence Scanning Package
- SCWRL 4.0 – Prediction of Protein Side-chain Conformation
- SecretomeP 2.0 – Prediction of Non-classical Protein Secretion
- Sfixem – SFS Visualisation Tool in Java
- SherLoc2 20091026 – Predicting Protein Subcellular Localization
- SIFT 4.0.4 – Amino Acid Substitution Affects Protein Function
- SignalP 4.0c – Predict Signal Peptides
- SMAP 2.0 – Comparison & Similarity Search of Protein Three-dimensional Motif
- SPICE 0.9 – Protein Sequences, Structures & Annotations Browser
- SPICKER 20101229 – Cluster Protein Structures for Near-native Model Selection
- STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam
- SubMito 1.1 – Predict Protein Submitochondria Locations from Sequence
- SVMSEQ 1.0 – Protein Contact Prediction
- TargetP 1.1 – Predict Protein Subcellular Localisation
- TESTLoc – Protein Localization Prediction based on ESTs
- TM-score 20110130 – Calculate Similarity of Topologies of two Protein Structures
- TMHMM 2.0c – Prediction of Transmembrane Helices in Proteins
- Topcons – Consensus Prediction of Membrane Protein Topology
- TOPO2 – Create Transmembrane Proteins Images
- TRUST 1.0 – Repeat Detection Method
- Utopia 1.4.5 – Protein Analysis Suite
- VDJsolver 1.0b – Analysis of Human Immunoglobulin VDJ Recombination
- VEMS 5.18042011 – Analysis of MS-based Proteomics Data
- VHMPT – Viewer & Editor for Helical Membrane Protein Topologies
- WinPep 3.01 – Analysis of Aminoacid Sequences
- Wise 2.2.0 – Compare Protein Sequence to Genomic DNA Sequence
- YinOYang 1.2 – O-(beta)-GlcNAc Glycosylation and Yin-Yang Sites
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