Databases – Proteomics

Molecular Modeling

• PDB – processing and distrubutio of 3D biological macromolecular structure data
• CATH – protein structure classification
• DALI – networking services for comparing protein structures in 3D
• DSSP – definition of secondary structure of proteins given a set of 3D coordinates
• FSSP – food classification based on structure-structure alignment of proteins
• HSSP Database – Homology-derived Secondary Structure of Proteins
• Jpred2 – method for protein secondary structure prediction
• K2 – protein structure alignment – various food recognition and local structure prediction methods
• PredictProtein & PHD – service for sequence analysis, and structure prediction
• PSIpred (& MEMSAT & GenTHREADER) – protein structure prediction server
• RasMol / Protein Explorer – software for viewing macromolecular structure
• SCOP – Structural Classification Of Proteins
• SWISS-MODEL – protein modeling server
• The DALI Domain Database – structure classification of protein domains
• The Proteome Databases – yeast, worm, & human, good annotation

Protein Sequence Databases

• PIR – Protein Information Resource
• SWISS-PROT & TrEMBL – protein sequence knowledge database and computer annotated supplement

Ribosomal Databases

• Silva – Ribosomal database based on ARB software
• RDP – Ribosomal Database Project (bacterial, archaeal and fungal)
• Greengenes – Microbial 16S ribosomal database