Bioinformatics & Genomics
Protein & Nucleic Acid Search Servers
Fold Recognition Methods
Sequence Database Search Servers
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[San Diego Supercomputer Center] The Conserved Key Amino Acid Positions database provides access to an analysis of structurally similar proteins with dissimilar sequences where key residues within a common fold are identified. CKAAP database provides CKAAPs of the representative set of proteins derived from the Combinatorial Extension algorithm and FSSP databases.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
[Analytical Biostatistics Section - NIH] "FORESST is a database (with search engine) of hidden Markov models that characterize secondary structure representations of protein structural domains."
FSSP: Fold classification based on Structure-Structure alignment of Proteins
[European Molecular Biology Laboratory] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
[Brunel University] This fold recognition method predicts protein structure via threading techniques and searches a fold library created from the Protein Data Bank (PDB).
The Live Bench Project is a continuous
benchmarking program. Every week new Protein Data Bank (PDB)
proteins are submitted to all participating
fold recognition servers. The results are
collected and evaluated using automated model
[SWBIC] Protein Classification through the Assessment of Predicted Secondary Structure (PCAPSS) is a method for identifying remote protein homologs in the Protein Data Bank that share a similar secondary
structure to the query protein. PCAPSS was designed to be used with orphan or hypothetical proteins, i.e.,
those for which amino acid sequence searches fail to find similar sequences with functional annotation. Its purpose
is to generate hypotheses for structure and function for such hypothetical or putative protein sequences based on
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
SCOP: Structural Classification of Proteins
[MRC Laboratory of Molecular Biology and Centre for Protein Engineering] Survey of known protein folds; information on close relatives of a given protein using keywords and homology searches.
UCLA/DOE Fold Server
[UCLA-DOE] Motif-Based Fold Assignment method combines the
functional information contained in the SwissProt keyword annotation with Prosite
motif database to improve the performance of any conventional
sequence/structure based prediction.