PROTEIN BIOINFORMATICS LINKS OF TODD TAYLOR ANALYSIS SUITES SDSC Biology Workbench EBI Toolbox BINDING/ACTIVE/FUNCTIONAL SITES CASTp Catalytic Site Atlas Catalytic Site Search ConSeq ConSurf Eukaryotic Linear Motif Evolutionary Trace Fuzzy-Oil-Drop HotPatch PINUP ProMate SARIG SiteEngine SOAK SUMO CONTACT ANALYSIS AND PREDICTION CNB-CSIC CSU EVAcon GPCPRED PoCM SAM-T06 SCRATCH DOCKING AND LIGAND INTERACTION AutoDock FTDock MSDsite UCSF DOCK DOMAIN/MOTIF ASSIGNMENT (SEQUENCE BASED) ADDA Blocks CHOP COGs CDD InterPro Pfam PRINTS ProDom PROSITE ProtoMap DOMAIN ASSIGNMENT (STRUCTURE BASED) 3Dee Anatomy BML Domain Server (expert assignment) BML Domain Server CATH DALI/FSSP DePot DDBASE Dial Domain3D DomainParser DOMAK ModDom PDOMAINS PDP PUU SCOP VAST DOMAIN PREDICTION DomPred SBASE Scooby-domain SCRATCH ELASTIC AND GAUSSIAN NETWORKS/NORMAL MODES AD-ENM Anisotropic Network Model ANM elNémo iGNM GNM Server oGNM ProMode ENZYMES BRENDA EC Numbers of PDB Entries Enzyme Structure Database EZCatDB Thermodynamics of Enzyme-Catalyzed Reactions FOLD RECOGNITION 123D 3D-PSSM bioinbgu FUGUE Libra I LOOPP PredictProtein SAM-T06 Sparks2 UCLA/DOE Fold Server WURST FUNCTION PREDICTION AUTO-MUTE ProFunc WebFEATURE GEOMETRY, VOLUMES, AND VOIDS AVP Delaunay Tessellation of Proteins VOIDOO HOMOLOGY MODELLING 3D-JIGSAW CPHmodels ESyPred3D MODELLER MolIDE SWISS-MODEL INTRINSICALLY DISORDERED REGIONS DisEMBL DISOPRED2 DISpro DISPROT DisProt DRIPPRED FoldIndex FoldUnfold GMU database GlobPlot IUPp Blender IUPred NORSP RONN SPRITZ LOOPS WLoop Homology Modeling MEMBRANE PROTEINS DAS Orientations of Proteins in Membranes TMHMM TopPred TransMembrane Protein DataBase MISCELLANEOUS TOOLS AND DATABASES Kyte-Doolittle Hydropathy Plots MaxSprout (reconstruct protein from C-alpha's) Molecular Weight and Isoelectric Point PAM Matrix Generation PDB Metrics Protein Property Calculator Protherm ProtScale Statistical Analysis of Protein Sequences Transeq (DNA to protein translation) WebLogo (sequence logos) MOLECULAR DYNAMICS/MECHANICS AMBER Biomer CHARMM GROMACS GROMOS MOIL NAMD TINKER MUTANT DATABASES MutaProt PMD NON-REDUNDANT TRAINING SETS PDBselect PISCES uniqueProt PROTEIN INTERACTION InterPreTS PPI-Pred PRISM Protein-Protein Interaction Server SCOPPI SPPIDER QUATERNARY STRUCTURE Protein Quaternary Structure Query Form at the EBI QuaternaryStructure Predictor SECONDARY STRUCTURE ASSIGNMENT DSSP (ftp directory of assignments) DSSP (server) DSSPcont HSSP KAKSI PALSSE PROSS P_SEA SSA STRIDE t4 (Delaunay tessellation based) Voro3D/VoTAP XTLsstr SECONDARY STRUCTURE PREDICTION APSSP2 CDM Secondary Structure Server EVA Jpred NPS@ PHD/Predict Protein PORTER PREDATOR PROF PSIPRED SABLE SAM-T06 SCRATCH YASPIN SEQUENCE ALIGNMENT PRALINE TCoffee SEQUENCE DATABASES NCBI protein sequence Swiss-Prot SIDE CHAINS sccomp SCWRL3 STRUCTURE CLASSIFICATION CATH DALI FSSP SCOP STRUCTURE COMPARISON/ALIGNMENT (PAIRWISE) CE DaliLite FAST FATCAT K2 LGA MAMMOTH MASS MATRAS MINAREA MultiProt Protein3d Protein3Dfit SALIGN SARF2 SCALI SCMBB SSAP SSM SuperPose TOPOFIT TOPS VAST URMS Yale LSQRMS STRUCTURE COMPARISON/ALIGNMENT (MULTIPLE) CE-MC MAMMOTH MASS MultiProt POSA SALIGN SSM URMS STRUCTURE DATABASES MMDB/NCBI Structure MSD OCA PDB PDBsum STRUCTURE DECOYS CASP predictions Decoys'R'Us Free Univ of Brussels I-TASSER Rosetta Sali comparative model decoys STRUCTURE VALIDATION Biotech Validation Suite (PROCHECK, WHAT IF, PROVE) Delaunay four-body sequence-structure compatibility ProSA-web SURFACE AND HYDRATION Analytic Surface Calculation Package CASTp GETAREA 1.1 pvSoar MSMS WESA VIEWERS Chimera DeepView Molecules To Go PDB to MultiGIF POLYVIEW-3D PyMOL RasMol VMD Todd Taylor Home Revised 8/14/2007