AS2TS system for protein structure modeling and analysis

• Published in: Nucleic acids research Vol. 33; no. suppl-2; pp. W111 - W115
• Main Authors: Zemla, A., Zhou, C. Ecale, Slezak, T., Kuczmarski, T., Rama, D., Torres, C., Sawicka, D., Barsky, D.
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-07-2005; Oxford Publishing Limited (England)
• Subjects: Capsid Proteins - chemistry; Databases, Protein; Internet; Models, Molecular; Protein Conformation; Sequence Analysis, Protein; Software; Structural Homology, Protein
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gki457

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/.