Protein Structures

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

• CPHmodels Server
• MODELLER
• SWISS-MODEL
• WHAT IF

Fold Recognition

• PROSPECT
• 123D
• CASP2 Evaluation of Fold-Recognition
• CASP3 Page
• NCBI Structure Group Threading Package
• SAM
• PredictProtein
• PSI-BLAST
• SAS (Sequences Annotated by Structure)
• THREADER
• ToPLign
• UCLA-DOE Fold-Recognition Server
• UCLA-DOE Benchmark To Assess Threading

Ab initio Prediction

• ProStar

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

• SCWRL
• MaxSprout server
• NAOMI

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)