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Protein Structure Prediction
Database
- PDB
- 3DinSight
- Cambridge Structural Database (CSD)
- Enhanced NCI Database Browser (Ligands)
- Enzyme Structures Database
- HSSP
- LIGAND
- Macromolecular Structure Database
- NRL_3D
- PDBsum
- PDB Select
- PROCAT (3D enzyme active site templates)
- ReLiBase
- PRESAGE
- WPDB
Homology Modeling
Fold Recognition
- PROSPECT
- 123D
- CASP3 Page
- NCBI Structure Group Threading Package
- SAM T-02
- PredictProtein
- FUGUE
- PSI-BLAST
- SAS (Sequences Annotated by Structure)
- GenTHREADER
- sDPSSM
- ToPLign
- UCLA-DOE Fold-Recognition Server
- UCLA-DOE Benchmark To Assess Threading
Ab initio Prediction
X-Ray/NMR Tools
- BioMagResBank
- CCP4: Macromolecular Crystallography
- ERRAT
- ESPOIR
- FANTOM
- NMRCLUST
- NMR Information Server
- O
- PROTEIN system
- Situs
- X-PLOR
Sidechain Prediction from Mainchain
Atomic Information
- WHAT IF (Mutant Prediction, Structure Verification, etc.)
- Atlas of Side-Chain and Main-Chain Hydrogen Bonding
- HBPLUS (Hydrogen Bond Calculation Program)
- HIPPO (Hydrogen Bonding Interaction Site Prediction)
- NAOMI
- Verify3D (Refinement of Crystallographic Structures)
Geometry
- ASC (Analytic Surface Calculation Package)
- GETAREA 1.0 (Calculation of Accessible Surface Areas and Solvation Energies)
- NACCESS (Atomic Solvent Accessible Area Calculations)
- Steric (Calculate the Steric Size of Molecules)
Protein Domains
- 3 Dee (Database of Protein Domain Definitions)
- Dali Domain Dictionary
- Protein Domain Server (Domain Assignment)
- Protein Motions Database
Structure Comparison/Classification
- Dali Server (Comparing Protein Structures in 3D)
- CATH (Protein Structure Classification)
- FSSP (Database of Families of Structurally Similar Proteins)
- HOMSTRAD (Homologous Structure Alignment Database)
- LPFC (A Library of Protein Family Cores)
- ProFit (Protein Least Squares Fitting Program)
- SARF (Spatial ARangement of backbone Fragments)
- SCOP (Structural Classification of Proteins)
- VAST/MMDB (Vector Alignment Search Tool)
- MaxSub
- CE