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PROSITE Patterns / Profiles
ProDom Aligned motifs (PSI-BLAST) (Pfam B)
PRINTS Aligned motifs
Pfam HMM (Hidden Markov Models)
DOMO Aligned motifs
BLOCKS Aligned motifs (PSI-BLAST)
CDD(CDART) PSI-BLAST(PSSM) of Pfam and SMART
use SWISS-PROT as a master index
EPO_HUMAN (human plasma)
Should be here…
HSSP: Homology-derived secondary structure of proteins.
FSSP: Fold Classification based on Structure-Structure Assignments.
Usualy these databases are tightly coupled with query software that allows the user to visualise reaction schemes.