PMP | Related Tools

Modeling Services:

  • ModWeb - Server for Comparative Protein Structure Modeling MedLine
  • M4T - M4T protein modeling server MedLine
  • PIGS - Automatic prediction of immunoglobulin structures
  • ProtMod - protein modeling server (JCMM)
  • PUDGE - Protein structure prediction server MedLine
  • RosettaAntibody - homology modeling server for predicting antibody Fv region structures MedLine
  • Robetta - Robetta provides both ab initio and comparative models of protein domains MedLine
  • I-Tasser Online - automated protein structure and function prediction MedLine
  • SWISS-MODEL - SWISS-MODEL Workspace for protein structure homology modeling MedLine
  • SCWRL - SCWRL Server (JCSG) MedLine
  • LifeExplorer - modeling of 3D protein-DNA assemblies /real-time navigation within the cell at various scales MedLine
  • Phyre2 - Protein Homology/analogY Recognition Engine - Protein structure prediction MedLine
  • RaptorX - Template-based protein structure modeling MedLine
  • SPARKSX - Fold Recognition MedLine

Template Selection / Fold Assignment / Function Prediction:

  • FFAS03 - Fold & Function Assignment System (JCMM) MedLine
  • PSCA - Protein Sequence Comparative Analysis (JCSG)
  • Predict Protein - sequence analysis, structure and function prediction (NESG) MedLine
  • LOMETS - local meta-threading-server for protein structure prediction MedLine
  • PUDGE - Protein structure prediction server MedLine
  • SWISS-MODEL - SWISS-MODEL Workspace template selection tools
  • SiteHound - server for ligand binding site identification in protein structures
  • genTHREADER - an efficient and reliable protein fold recognition method for genomic sequences

Structure / Model Quality Evaluation:

  • ANOLEA - Atomic Non-Local Environment Assessment
  • ConQuass - ConQuass webserver
  • DFIRE2 - Protein Conformation Free Energy Score
  • MetaMQAP - Meta Model Quality Assessment server
  • ModFOLD - ModFOLD Model Quality Assessment Server
  • ProQ - ProQ Protein Quality Predictors
  • ProSA - ProSA-web Protein Structure Analysis
  • PSQS - Protein Structure Quality Score (JCMM)
  • PSVS - Protein Structure Validation Software suite (NESG)
  • QMEAN - QMEAN Server for Model Quality Estimation (SIB)
  • SelectPro - protein model selection using a structure-based energy function resistant to blunders
  • ModEval - Model Evaluation Server (Sali Lab)
  • SWISS-MODEL - SWISS-MODEL Workspace protein structure assessment tools (SIB)
  • Verify3D - Structure evluation server

Protein Structure Alignment, Comparison and Classification:

  • CATH - Protein Structure Classification MedLine
  • FATCAT - Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (JCMM) MedLine
  • POSA - Partial Order Structure Alignment (JCMM) MedLine