AS2TS system for protein structure modeling and analysis | Zendy

Adam Zemła | Zendy; Chen Zhou | Zendy; T. Šlezak | Zendy; Tom Kuczmarski | Zendy; D. Rama | Zendy; Cristiane Batista Bezerra Torres | Zendy; Dorota Sawicka | Zendy; Daniel Barsky | Zendy

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AS2TS system for protein structure modeling and analysis

Author(s) -

Adam Zemła,

Chen Zhou,

T. Šlezak,

Tom Kuczmarski,

D. Rama,

Cristiane Batista Bezerra Torres,

Dorota Sawicka,

Daniel Barsky

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki457

Subject(s) - protein data bank (rcsb pdb) , protein data bank , protein structure database , homology modeling , protein structure , protein structure prediction , structural alignment , loop modeling , biology , sequence alignment , computational biology , protein tertiary structure , similarity (geometry) , set (abstract data type) , sequence analysis , threading (protein sequence) , sequence (biology) , bioinformatics , peptide sequence , sequence database , computer science , genetics , programming language , biochemistry , artificial intelligence , dna , gene , image (mathematics) , enzyme

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence-structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at http://as2ts.llnl.gov/.

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