ProDy Logo
  • Installation
    • Required Software
    • Quick Install
    • Installing From Source (not recommended)
    • Recommended Software
    • Included in ProDy
    • Source Code
  • Applications
    • ProDy Applications
      • prody align
        • Usage
        • Examples
      • prody anm
        • Usage
        • Examples
      • prody biomol
        • Usage
        • Examples
      • prody blast
        • Usage
        • Examples
      • prody catdcd
        • Usage
        • Examples
      • prody contacts
        • Usage
        • Examples
      • prody eda
        • Usage
        • Examples
      • prody fetch
        • Usage
        • Examples
      • prody gnm
        • Usage
        • Examples
      • prody pca
        • Usage
        • Examples
      • prody select
        • Usage
        • Examples
    • Evol Applications
      • evol coevol
        • Usage
        • Examples
      • evol conserv
        • Usage
        • Examples
      • evol fetch
        • Usage
        • Examples
      • evol filter
        • Usage
        • Examples
      • evol merge
        • Usage
        • Examples
      • evol occupancy
        • Usage
        • Examples
      • evol rankorder
        • Usage
        • Examples
      • evol refine
        • Usage
        • Examples
      • evol search
        • Usage
        • Examples
  • Reference Manual
    • Atomic Data
      • Atomic classes
      • Atom data fields
      • Atom flags
      • Atom selections
      • Functions
      • Hydrogen Bond Acceptor
        • Acceptor
      • Angle
        • Angle
      • Atom
        • Atom
      • Atom Group
        • AtomGroup
      • Atomic Base
        • Atomic
      • Atom Map
        • How AtomMap works
        • AtomMap
      • Bond
        • Bond
      • Chain
        • Chain
      • Cross-term
        • Crossterm
      • Dihedral
        • Dihedral
      • Hydrogen Bond Donor
        • Donor
      • Atom Data Fields
        • Field
      • Atom Flags
        • Protein
        • Nucleic
        • Heteros
        • Elements
        • Structure
        • Others
        • addNonstdAminoacid()
        • delNonstdAminoacid()
        • flagDefinition()
        • getNonstdProperties()
        • listNonstdAAProps()
      • Supporting Functions
        • extendAtomicData()
        • extendAtoms()
        • findFragments()
        • isReserved()
        • iterFragments()
        • listReservedWords()
        • loadAtoms()
        • saveAtoms()
        • sliceAtomicData()
        • sliceAtoms()
        • sortAtoms()
      • Hierarchical Views
        • HierView
      • Improper
        • Improper
      • Non-Bonded Exclusions
        • NBExclusion
      • Atom Pointer
        • AtomPointer
      • Residue
        • Residue
      • Segment
        • Segment
      • Atom Selections
        • Atom flags
        • Logical operators
        • Quick selections
        • Atom data fields
        • Numerical comparisons
        • Distance based selections
        • Sequence selections
        • Expanding selections
        • Selection macros
        • Select
        • SelectionError
        • SelectionWarning
        • defSelectionMacro()
        • delSelectionMacro()
        • getSelectionMacro()
        • isSelectionMacro()
      • Selection
        • Selection
      • Atom Subsets
        • AtomSubset
    • Chromatin Dynamics Analysis
      • Parse/write Hi-C files
      • Visualize Hi-C data
        • Save/load HiC class
      • Chromatin clustering
        • BayesianGaussianMixture()
        • Discretize()
        • GaussianMixture()
        • Hierarchy()
        • KMeans()
        • calcGNMDomains()
        • showLinkage()
      • Chromatin functions
        • getDomainList()
        • showDomains()
        • showEmbedding()
      • HiC
        • HiC
        • loadHiC()
        • parseHiC()
        • parseHiCStream()
        • saveHiC()
        • writeMap()
      • Chromatin normalization
        • Filenorm()
        • SCN()
        • SQRTVCnorm()
        • VCnorm()
      • Straw HiC API
        • getBlockNumbersForRegionFromBinPosition()
        • printme()
        • readBlock()
        • readFooter()
        • readHeader()
        • readMatrix()
        • readMatrixZoomData()
        • readNormalizationVector()
        • straw()
    • Compounds Analysis
      • Ligand data
      • BIRD data
      • CCD data
      • Functions
      • BIRD Classes and Functions
        • fetchBIRDviaFTP()
        • parseBIRD()
      • CCD Classes and Functions
        • parseCCD()
      • Supporting Functions
        • calc2DSimilarity()
      • PDB Ligands
        • PDBLigandRecord
        • fetchPDBLigand()
        • parsePDBLigand()
    • Database Support
      • Pfam
      • UniProt
      • CATH
      • DALI
      • QuartataWeb
      • Gene Ontology Annotation (GOA)
      • Interpro
      • BioExcel-CV19
      • CATH Access Functions
        • CATHDB
        • CATHElement
      • Dali Server Functions
        • DaliRecord
        • daliFilterMultimer()
        • daliFilterMultimers()
        • searchDali()
      • Gene Ontology Annotation (GOA) Server Functions
        • GOADictList
        • calcDeepFunctionOverlaps()
        • calcEnsembleFunctionOverlaps()
        • calcGoOverlap()
        • calcMinBranchLength()
        • findCommonParentGoIds()
        • findDeepestCommonAncestor()
        • findDeepestFunctions()
        • parseGAF()
        • parseOBO()
        • queryGOA()
        • showGoLineage()
      • Pfam Access Functions
        • fetchPfamMSA()
        • parsePfamPDBs()
        • searchPfam()
      • QuartataWeb Server Functions
        • QuartataChemicalRecord
        • QuartataWebBrowser
        • searchQuartataWeb()
      • UniProt Access Functions
        • UniprotRecord
        • queryUniprot()
        • searchUniprot()
    • Dynamical Domain Decomposition
      • Spectrus
    • Dynamics Analysis
      • Dynamics Models
      • Customize ENMs
      • Membrane Models
      • Signature Dynamics (SignDy)
      • Function library
      • Analyze models
      • Compare models
      • Generate conformers
      • Adaptive ANM
      • ENM-MD hybrid methods
      • Essential Site Scanning Analysis (ESSA)
      • Editing models
      • Parse/write data
      • Save/load models
      • Short-hand functions
      • Plotting functions
      • Heat Mapper support
      • Visualize modes
      • Adaptive ANM
        • calcAdaptiveANM()
      • Analysis Functions
        • calcAnisousFromModel()
        • calcCollectivity()
        • calcCovariance()
        • calcCrossCorr()
        • calcCrossProjection()
        • calcDistFlucts()
        • calcFractVariance()
        • calcHemnmaScore()
        • calcHinges()
        • calcHitTime()
        • calcMostMobileNodes()
        • calcPairDeformationDist()
        • calcProjection()
        • calcRMSFlucts()
        • calcScipionScore()
        • calcSpecDimension()
        • calcSqFlucts()
        • calcTempFactors()
        • getGlobalHinges()
        • getHinges()
      • Anisotropic Network Model
        • ANM
        • MaskedANM
        • calcANM()
      • ANMD simulations
        • runANMD()
      • ClustENM(D) simulations
        • ClustENM
        • ClustExANM
        • ClustImANM
        • ClustRTB
      • Comparison Functions
        • calcCovOverlap()
        • calcCumulOverlap()
        • calcOverlap()
        • calcRMSIP()
        • calcRWSIP()
        • calcSIP()
        • calcSpectralOverlap()
        • calcSquareInnerProduct()
        • calcSubspaceOverlap()
        • matchModes()
        • pairModes()
        • printOverlapTable()
        • writeOverlapTable()
      • NMA Model Editing
        • extendMode()
        • extendModel()
        • extendVector()
        • interpolateModel()
        • reduceModel()
        • reduceModelByMask()
        • sliceMode()
        • sliceModel()
        • sliceModelByMask()
        • sliceVector()
        • trimModel()
        • trimModelByMask()
      • Essential Site Scanning Analysis
        • ESSA
      • Explicit Membrane Anisotropic Network Model
        • exANM
      • Explicit Membrane Gaussian Network Model
        • exGNM
      • Supporting Functions
        • calcENM()
        • loadModel()
        • loadVector()
        • parseArray()
        • parseGromacsModes()
        • parseModes()
        • parseScipionModes()
        • parseSparseMatrix()
        • realignModes()
        • saveModel()
        • saveVector()
        • writeArray()
        • writeModes()
        • writeScipionModes()
      • Custom Gamma Functions
        • Gamma
        • GammaED
        • GammaGOdMD
        • GammaStructureBased
        • GammaVariableCutoff
      • Gaussian Network Model
        • GNM
        • MaskedGNM
        • calcGNM()
      • Heatmapper Functions
        • parseHeatmap()
        • showHeatmap()
        • writeHeatmap()
      • Implicit Membrane Anisotropic Network Model
        • imANM
      • Mechanical Stiffness Calculations
        • calcMechStiff()
        • calcMechStiffStatistic()
        • calcStiffnessRange()
        • calcStiffnessRangeSel()
      • Normal Mode
        • Mode
        • Vector
      • Mode Set
        • ModeSet
      • Normal Mode Analysis
        • MaskedNMA
        • NMA
      • NMD File
        • NMD Format
        • getVMDpath()
        • parseNMD()
        • pathVMD()
        • setVMDpath()
        • viewNMDinVMD()
        • writeNMD()
      • Principal Component Analysis
        • EDA
        • PCA
      • Perturbation Response Scanning
        • calcDynamicCouplingIndex()
        • calcDynamicFlexibilityIndex()
        • calcPerturbResponse()
      • Plotting Functions
        • pimshow()
        • pplot()
        • resetTicks()
        • showAtomicBars()
        • showAtomicLines()
        • showAtomicMatrix()
        • showContactMap()
        • showCovarianceMatrix()
        • showCrossCorr()
        • showCrossProjection()
        • showCumulFractVars()
        • showCumulOverlap()
        • showDiffMatrix()
        • showDomainBar()
        • showEllipsoid()
        • showFractVars()
        • showMeanMechStiff()
        • showMechStiff()
        • showMode()
        • showNormDistFunct()
        • showNormedSqFlucts()
        • showOverlap()
        • showOverlapTable()
        • showOverlaps()
        • showPairDeformationDist()
        • showPerturbResponse()
        • showProjection()
        • showRMSFlucts()
        • showScaledSqFlucts()
        • showSelectionMatrix()
        • showSqFlucts()
        • showTree()
        • showTree_networkx()
      • Rotation Translation Blocks
        • RTB
      • Sampling Functions
        • deformAtoms()
        • sampleModes()
        • traverseMode()
      • Signature Dynamics of Protein Families (SignDy)
        • ModeEnsemble
        • calcEnsembleENMs()
        • calcEnsembleSpectralOverlaps()
        • calcSignatureCollectivity()
        • calcSignatureCrossCorr()
        • calcSignatureFractVariance()
        • calcSignatureModes()
        • calcSignatureOverlaps()
        • calcSignaturePerturbResponse()
        • calcSignatureSqFlucts()
        • calcSubfamilySpectralOverlaps()
        • loadModeEnsemble()
        • loadSignature()
        • psplot()
        • saveModeEnsemble()
        • saveSignature()
        • sdarray
        • showSignature1D()
        • showSignatureAtomicLines()
        • showSignatureCollectivity()
        • showSignatureCrossCorr()
        • showSignatureDistribution()
        • showSignatureMode()
        • showSignatureOverlaps()
        • showSignatureSqFlucts()
        • showSignatureVariances()
        • showSubfamilySpectralOverlaps()
        • showVarianceBar()
      • Writing TCL scripts for VMD
        • calcChainsNormDistFluct()
        • writeDeformProfile()
        • writeVMDstiffness()
    • Ensemble Analysis
      • Conformational ensembles
      • PDB ensembles
      • Save/load ensembles
      • Conformation
        • Conformation
        • PDBConformation
      • Conformational Ensemble
        • Ensemble
      • Supporting Functions
        • alignByEnsemble()
        • buildPDBEnsemble()
        • calcOccupancies()
        • combineEnsembles()
        • loadEnsemble()
        • refineEnsemble()
        • saveEnsemble()
        • showOccupancies()
        • trimPDBEnsemble()
      • PDB Structure Ensemble
        • PDBEnsemble
    • KDTree
      • KD Tree
        • KDTree
    • Measurement Tools
      • Identify contacts
      • Measure quantities
      • Anisotropic factors
      • Transformations
      • Contact Identification
        • Contacts
        • findNeighbors()
        • iterNeighbors()
      • Measurement Tools
        • assignBlocks()
        • buildADPMatrix()
        • buildDistMatrix()
        • calcADPAxes()
        • calcADPs()
        • calcAngle()
        • calcCenter()
        • calcDeformVector()
        • calcDihedral()
        • calcDistance()
        • calcDistanceMatrix()
        • calcGyradius()
        • calcInertiaTensor()
        • calcMSF()
        • calcOmega()
        • calcPhi()
        • calcPrincAxes()
        • calcPsi()
        • calcRMSF()
        • getAngle()
        • getDihedral()
        • pickCentral()
        • pickCentralAtom()
        • pickCentralConf()
      • Transformations
        • Transformation
        • alignCoordsets()
        • applyTransformation()
        • calcRMSD()
        • calcTransformation()
        • moveAtoms()
        • printRMSD()
        • superpose()
        • wrapAtoms()
    • Protein Structure
      • PDB resources
      • Blast search PDB
      • Parse/write PDB files
      • Parse mmCIF files
      • Quick visualization
      • Edit structures
      • PDB header data
      • Analyze interactions and stability with InSty and find water bridges with WatFinder
      • Detect channels, tunnels and pores with CaviFinder
      • Compare/align chains
      • Execute DSSP
      • Execute STRIDE
      • Handle EMD Map Files and Build Pseudoatoms into them
      • Add missing atoms including hydrogens
      • PDB Blast Search
        • PDBBlastRecord
        • blastPDB()
      • mmCIF File
        • parseCIF()
        • parseMMCIF()
        • parseMMCIFStream()
        • writeMMCIF()
      • Structure Comparison
        • alignChains()
        • bestMatch()
        • combineAtomMaps()
        • getAlignmentMethod()
        • getGapExtPenalty()
        • getGapPenalty()
        • getGoodCoverage()
        • getGoodSeqId()
        • getMatchScore()
        • getMismatchScore()
        • mapChainOntoChain()
        • mapOntoChain()
        • mapOntoChainByAlignment()
        • mapOntoChains()
        • matchAlign()
        • matchChains()
        • sameChainPos()
        • sameChid()
        • setAlignmentMethod()
        • setGapExtPenalty()
        • setGapPenalty()
        • setGoodCoverage()
        • setGoodSeqId()
        • setMatchScore()
        • setMismatchScore()
        • userDefined()
      • DSSP Tools
        • execDSSP()
        • parseDSSP()
        • performDSSP()
      • EMD File
        • EMDMAP
        • TRNET
        • parseEMD()
        • parseEMDStream()
        • writeEMD()
      • Miscellaneous Tools
        • showProtein()
        • view3D()
      • PDB File Header
        • Chemical
        • DBRef
        • Polymer
        • assignSecstr()
        • buildBiomolecules()
        • parsePDBHeader()
      • Interactions and Stability (InSty)
        • Interactions
        • InteractionsTrajectory
        • LigandInteractionsTrajectory
        • calcChHydrogenBonds()
        • calcDistribution()
        • calcDisulfideBonds()
        • calcDisulfideBondsTrajectory()
        • calcHydrogenBonds()
        • calcHydrogenBondsTrajectory()
        • calcHydrophobic()
        • calcHydrophobicOverlapingAreas()
        • calcHydrophobicTrajectory()
        • calcLigandInteractions()
        • calcMetalInteractions()
        • calcPiCation()
        • calcPiCationTrajectory()
        • calcPiStacking()
        • calcPiStackingTrajectory()
        • calcProteinInteractions()
        • calcRepulsiveIonicBonding()
        • calcRepulsiveIonicBondingTrajectory()
        • calcSASA()
        • calcSaltBridges()
        • calcSaltBridgesTrajectory()
        • calcSignatureInteractions()
        • calcSminaBindingAffinity()
        • calcSminaPerAtomInteractions()
        • calcSminaTermValues()
        • calcStatisticsInteractions()
        • calcVolume()
        • checkNonstandardResidues()
        • compareInteractions()
        • createFoldseekAlignment()
        • extractMultiModelPDB()
        • listLigandInteractions()
        • runBLAST()
        • runDali()
        • runFoldseek()
        • saveInteractionsAsDummyAtoms()
        • showInteractionsGraph()
        • showInteractionsHist()
        • showLigandInteraction()
        • showLigandInteraction_VMD()
        • showPairEnergy()
        • showProteinInteractions()
        • showProteinInteractions_VMD()
        • showSminaTermValues()
      • Local PDB Handlers
        • fetchPDB()
        • fetchPDBfromMirror()
        • fetchPDBs()
        • findPDBFiles()
        • iterPDBFilenames()
        • pathPDBFolder()
        • pathPDBMirror()
      • PDB Sequence Clusters
        • fetchPDBClusters()
        • listPDBCluster()
        • loadPDBClusters()
      • PDB File
        • parseChainsList()
        • parsePDB()
        • parsePDBStream()
        • parsePQR()
        • writeChainsList()
        • writePDB()
        • writePDBStream()
        • writePQR()
        • writePQRStream()
      • STAR File
        • StarDataBlock
        • StarDict
        • StarLoop
        • parseImagesFromSTAR()
        • parseSTAR()
        • parseSTARSection()
        • writeSTAR()
      • Stride Tools
        • execSTRIDE()
        • parseSTRIDE()
        • performSTRIDE()
      • Water bridge finder (WatFinder)
        • calcBridgingResiduesHistogram()
        • calcWaterBridgeMatrix()
        • calcWaterBridges()
        • calcWaterBridgesDistribution()
        • calcWaterBridgesStatistics()
        • calcWaterBridgesTrajectory()
        • filterStructuresWithoutWater()
        • findClusterCenters()
        • findCommonSelectionTraj()
        • getWaterBridgeStatInfo()
        • getWaterBridgesInfoOutput()
        • parseWaterBridges()
        • savePDBWaterBridges()
        • savePDBWaterBridgesTrajectory()
        • saveWaterBridges()
        • selectSurroundingsBox()
        • showWaterBridgeMatrix()
      • wwPDB Tools
        • fetchPDBviaFTP()
        • fetchPDBviaHTTP()
        • wwPDBServer()
    • Sequence Analysis
      • Classes
      • MSA IO
      • Editing
      • Analysis
      • Plotting
      • Analysis Functions
        • alignSequenceToMSA()
        • alignSequencesByChain()
        • alignTwoSequencesWithBiopython()
        • applyMutinfoCorr()
        • applyMutinfoNorm()
        • buildDirectInfoMatrix()
        • buildMSA()
        • buildMutinfoMatrix()
        • buildOMESMatrix()
        • buildPCMatrix()
        • buildSCAMatrix()
        • buildSeqidMatrix()
        • calcMSAOccupancy()
        • calcMeff()
        • calcPercentIdentities()
        • calcRankorder()
        • calcShannonEntropy()
        • filterRankedPairs()
        • showAlignment()
        • trimAtomsUsingMSA()
        • uniqueSequences()
      • Multiple Sequence Alignment
        • MSA
        • mergeMSA()
        • refineMSA()
        • specMergeMSA()
      • MSA File
        • MSAFile
        • parseMSA()
        • splitSeqLabel()
        • writeMSA()
      • Plotting Functions
        • showDirectInfoMatrix()
        • showMSAOccupancy()
        • showMutinfoMatrix()
        • showSCAMatrix()
        • showShannonEntropy()
      • Sequence
        • Sequence
    • Trajectory I/O
      • Parse/write DCD files
      • Parse structure files
      • Handle multiple files
      • Handle frame data
      • DCD File
        • DCDFile
        • parseDCD()
        • writeDCD()
      • Frame
        • Frame
      • PSF File
        • parsePSF()
        • writePSF()
      • Trajectory Base
        • TrajBase
      • Trajectory
        • Trajectory
      • Trajectory File
        • TrajFile
    • ProDy Utilities
      • Package utilities
      • Type/Value checkers
      • Path/file handling
      • Documentation tools
      • Miscellaneous tools
      • Tree Construction Tools
        • DistanceMatrix
        • DistanceTreeConstructor
        • TreeConstructor
      • Additional utilities
        • calcGromacsClusters()
        • calcGromosClusters()
        • calcRMSDclusters()
        • calcTree()
        • clusterMatrix()
        • clusterSubfamilies()
        • findSubgroups()
        • getCoords()
        • getLinkage()
        • getTreeFromLinkage()
        • printAtomicMatrix()
        • reorderMatrix()
        • showBars()
        • showLines()
        • showMatrix()
      • Type Checkers
        • checkAnisous()
        • checkCoords()
        • checkTypes()
        • checkWeights()
      • Documentation Tools
        • joinLinks()
        • joinRepr()
        • joinTerms()
        • tabulate()
        • wrapText()
      • Drawing/Plotting Tools
        • Arrow3D
        • IndexFormatter
        • drawTree()
      • Eigen Decomposition Tools
      • Linear Assignment Problems Tools
        • SolutionDepletionException
        • multilap()
      • Package Logger
        • PackageLogger
      • Miscellaneous Tools
        • Everything
        • addEnds()
        • alnum()
        • bin2dec()
        • checkIdentifiers()
        • countBytes()
        • decToHybrid36()
        • dictElement()
        • div0()
        • fixArraySize()
        • hybrid36ToDec()
        • impLoadModule()
        • importDec()
        • importLA()
        • intorfloat()
        • isPDB()
        • isSymmetric()
        • isURL()
        • makeSymmetric()
        • rangeString()
        • showFigure()
        • sqrtm()
        • startswith()
        • wmean()
      • Path Tools
        • addext()
        • backupFile()
        • copyFile()
        • glob()
        • gunzip()
        • isExecutable()
        • isReadable()
        • isWritable()
        • makePath()
        • openDB()
        • openFile()
        • openSQLite()
        • openURL()
        • pickle()
        • relpath()
        • sympath()
        • unpickle()
        • which()
      • Sequence Tools
        • alignBioPairwise()
        • splitSeqLabel()
      • Package Settings
        • PackageSettings
        • getPackagePath()
        • setPackagePath()
    • Applications API
      • Dynamics analysis
      • Structure analysis
      • Sequence analysis
      • Coevolution Application
        • evol_coevol()
      • Conservation Application
        • evol_conserv()
      • Pfam MSA Fetcher
        • evol_fetch()
      • MSA File Filter
        • evol_filter()
      • MSA File Merger
        • evol_merge()
      • MSA Occupancy Calculation
        • evol_occupancy()
      • Identify Coevolving Pairs
        • evol_rankorder()
      • MSA Refinement
        • evol_refine()
      • Pfam Search
        • evol_search()
      • PDB Model/Structure Alignment
        • prody_align()
      • ANM Application
        • prody_anm()
      • Biomolecule Builder
        • prody_biomol()
      • Blast Search PDB
        • prody_blast()
      • DCD Files Concatenation
        • prody_catdcd()
      • ANM Application
        • prody_clustenm()
      • Contact Identification
        • prody_contacts()
      • PDB File Fetcher
        • prody_fetch()
      • GNM Application
        • prody_gnm()
      • PCA Application
        • prody_pca()
      • Atom Selection
        • prody_select()
    • Configuration & Logging
      • confProDy()
      • checkUpdates()
      • startLogfile()
      • closeLogfile()
      • plog()
  • Developer’s Guide
    • Contributing to ProDy
      • Install Git and a GUI
      • Fork and Clone ProDy
      • Setup Working Environment
      • Modify, Test, and Commit
      • Push and Pull Request
      • Update Local Copy
    • Documenting ProDy
      • Building Manual
      • Building Website
    • How to Make a Release
    • Style Guide for ProDy
      • Introduction
      • Code Layout
      • Whitespaces
      • Naming Conventions
      • Variable Names
    • Testing ProDy
      • Running Unittests
      • Unittest Development
    • Writing Tutorials
      • Tutorial Setup
      • Style and Organization
      • Input/Output Files
      • Including Code
      • Including Figures
      • Testing Code
      • Publishing Tutorial
    • Building the Website
      • Environment Setup
      • Updating from GitHub
      • Publishing Changes
    • Making Windows Installers
    • Cross-platform Issues
      • Numpy integer type
      • Relative paths
  • Release Notes
    • ProDy 2.5 Series
      • 2.5.0 (Aug 14, 2024)
    • ProDy 2.4 Series
      • 2.4.1 (Aug 11, 2023)
      • 2.4.0 (Feb 2, 2023)
    • ProDy 2.3 Series
      • 2.3.1 (Nov 15, 2022)
      • 2.3.0 (Nov 12, 2022)
    • ProDy 2.2 Series
      • 2.2.0 (May 19, 2022)
    • ProDy 2.1 Series
      • 2.1.2 (April 27, 2022)
      • 2.1.1 (April 18, 2022)
      • 2.1.0 (April 8, 2022)
    • ProDy 2.0 Series
      • 2.0.2 (February 17, 2022)
      • 2.0.1 (Dec 20, 2021)
      • 2.0 (Dec 30, 2020)
    • ProDy 1.11 Series
      • 1.11 (Oct 1, 2020)
    • ProDy 1.10 Series
      • 1.10.11 (Oct 25, 2019)
      • 1.10.10 (May 9, 2019)
      • 1.10.9 (May 2, 2019)
      • 1.10.8 (Sept 18, 2018)
      • 1.10.7 (May 21, 2018)
      • 1.10.4 (May 15, 2018)
      • 1.10.3 (May 14, 2018)
      • 1.10.2 (May 2, 2018)
      • 1.10.1 (May 1, 2018)
      • 1.10 (Apr 30, 2018)
        • Signature Dynamics
    • ProDy 1.9 Series
      • 1.9.4 (Feb 02, 2018)
      • 1.9.3 (Oct 09, 2017)
      • 1.9.2 (Aug 29, 2017)
      • 1.9.1 (Aug 18, 2017)
      • 1.9 (May 23, 2017)
    • ProDy 1.8 Series
      • 1.8.2 (Jun 5, 2016)
      • 1.8.1 (May 28, 2016)
      • 1.8 (May 13, 2016)
        • MechStiff
    • ProDy 1.7 Series
      • 1.7.1 (May 31, 2015)
      • 1.7 (Dec 23, 2013)
    • ProDy 1.6 Series
      • 1.6.1 (May 31, 2015)
      • 1.5 (Dec 23, 2013)
    • ProDy 1.5 Series
      • 1.5.1 (Dec 24, 2013)
      • 1.5 (Dec 23, 2013)
    • ProDy 1.4 Series
      • 1.4.9 (Nov 14, 2013)
      • 1.4.8 (Nov 4, 2013)
      • 1.4.7 (Oct 29, 2013)
      • 1.4.6 (Oct 16, 2013)
      • 1.4.5 (Sep 6, 2013)
      • 1.4.4 (July 22, 2013)
      • 1.4.3 (June 14, 2013)
      • 1.4.2 (April 19, 2013)
      • 1.4.1 (Dec 16, 2012)
        • Normal Mode Wizard
      • 1.4 (Dec 2, 2012)
    • ProDy 1.3 Series
      • 1.3.1 (Nov 6, 2012)
      • 1.3 (Sep 30, 2012)
    • ProDy 1.2 Series
      • 1.2.1 (Sep 6, 2012)
      • 1.2 (Aug 30, 2012)
        • Normal Mode Wizard
    • ProDy 1.1 Series
      • 1.1 (June 1, 2012)
        • Normal Mode Wizard
    • ProDy 1.0 Series
      • 1.0.4 (May 2, 2012)
      • 1.0.3 (May 1, 2012)
      • 1.0.2 (May 1, 2012)
      • 1.0.1 (Apr 6, 2012)
      • 1.0 (Mar 7, 2012)
    • ProDy 0.9 Series
      • 0.9.4 (Feb 4, 2012)
      • 0.9.3 (Feb 1, 2012)
      • 0.9.2 (Jan 11, 2012)
      • 0.9.1 (Nov 9, 2011)
      • 0.9 (Nov 8, 2011)
        • Normal Mode Wizard
    • ProDy 0.8 Series
      • 0.8.3 (Oct 16, 2011)
      • 0.8.2 (Oct 14, 2011)
      • 0.8.1 (Sep 16, 2011)
        • Normal Mode Wizard
      • 0.8 (Aug 24, 2011)
        • nmwiz
    • ProDy 0.7 Series
      • 0.7.2 (Jun 21, 2011)
      • 0.7.1 (Apr 28, 2011)
      • 0.7 (Apr 4, 2011)
        • Normal Mode Wizard
    • ProDy 0.6 Series
      • 0.6.2 (Mar 16, 2011)
      • 0.6.1 (Mar 2, 2011)
      • 0.6 (Feb 22, 2011)
        • Normal Mode Wizard
    • ProDy 0.5 Series
      • 0.5.3 (Feb 11, 2011)
      • 0.5.2 (Jan 12, 2011)
      • 0.5.1 (Dec 31, 2010)
      • 0.5 (Dec 21, 2010)
    • ProDy 0.2 Series
      • 0.2 (Nov 16, 2010)
        • Normal Mode Wizard
    • ProDy 0.1 Series
      • 0.1.2 (Nov 9, 2010)
      • 0.1.1 (Nov 8, 2010)
      • 0.1 (Nov 7, 2010)
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