Databases

• Prolinks Database: A database of proteins having functional linkages to an input protein.
• DIP: Database of Interacting Proteins
• Protein Triples
• Structural Genomics of Mycobacterium tuberculosis
• MTBreg: the regulated Mtb proteins
• DAPS: Database of Aligned Protein Structures
• HIV and Alternative Splicing Databases

Data → Structure

• Merohedral Crystal Twinning Test
• Surface Entropy Reduction (SER) server:
  Identification of mutations designed to
  enhance protein crystallizability
• SAVes: Structure Analysis and Verification server
• Verify3D Structure Evaluation
• ERRAT Protein Structure Evaluation

               Sequence → Structure

• Bayesian Inference of Residue Contacts
• FAD or NADP binding Rossmann fold detector
• Fold Recognition
• Internal Repeat Finder
• MOMENT Transmembrane Helix Prediction
• Motif-Based Fold Assignment
• DPANN: Sequence to Structure Alignment
• Profile Search Software: Bowie et al. 1991
• Surface Entropy Reduction Crystallization Server

Sequence → Function

• Domain Fusion and Functionally Related Proteins
• Functional inferrence for yeast proteins
  on a genomic scale from multiple networks
• Genome-wide Prediction of Yeast Protein Function
• Mitochondrial Protein Prediction
• Partial Order Alignment
• Rare Codon Calculator

Structure → Function

• 3D Cluster Analysis of
  Functional Protein Sites
• HotPatch: Find functionally important
  patches on structures
• ProKnow: A server to suggest functions and annotations for a
  protein of known structure