Protein structure

• Automatic classification of protein structure by using gaussian integrals
• Mathematics Clinic on Computational Biology
• optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem
• Comparing Genomies in terms of Protein Structure
• A server for Structures Clustering, Averaging  and Refinement

Protein Sequence Clustering

• CLUSEQ: Efficient and Effective Sequence Clustering (ICDE'03)
• BAG: A Graph Theoretic Sequence Clustering Algorithm (01)

Protein Sequences Classification

• Protein Sequences Classification Based on String Weighting Scheme  Nazar M. Zaki, Safaai Deris and Rosli Illias
• A discriminative framework for detecting remote protein homologies (1999)  Tommi Jaakkola, Mark Diekhans, David Haussler
• Using the Fisher kernel method to detect remote protein homologies (1999)

(25 citations) Tommi Jaakkola, Mark Diekhans, David Haussle