02500nas a2200253   4500008004100000245008800041210006900129300000700198490001400205520139900219653007701618653005701695653019901752653003901951653002701990100002402017700001402041700002402055700001802079700001502097700001502112700001302127856010602140       2007                        eng d00aThe AnnoLite and AnnoLyze programs for comparative annotation of protein structures0 aAnnoLite and AnnoLyze programs for comparative annotation of pro  aS40 v8 Suppl 43 aBACKGROUND: Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database. DESCRIPTION: AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of  90% and average precision of  80%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of  70% and average precision of  30%, correctly localizing binding sites for small molecules in  95% of its predictions. CONCLUSION: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/.10a*Algorithms Amino Acid Sequence Confidence Intervals Data Interpretation10aAmino Acid *Software Structure-Activity Relationship10aProtein Information Storage and Retrieval/methods Molecular Sequence Data Proteins/*chemistry/classification/*metabolism Sensitivity and Specificity Sequence Alignment/*methods Sequence Analysis10aProtein/*methods Sequence Homology10aStatistical *Databases1 aMarti-Renom, M., A.1 aRossi, A.1 aAl-Shahrour, Fatima1 aDavis, F., P.1 aPieper, U.1 aDopazo, J.1 aSali, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1757014702151nas a2200277   4500008004100000245005200041210005100093300001100144490000700155520104000162653008701202653005701289653019401346653003901540653002701579100002401606700001501630700002401645700001401669700001401683700001801697700002401715700001501739700001301754856010601767       2007                        eng d00aDBAli tools: mining the protein structure space0 aDBAli tools mining the protein structure space  aW393-70 v353 aThe DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.10a*Algorithms Amino Acid Sequence Computational Biology/*methods Data Interpretation10aAmino Acid *Software Structure-Activity Relationship10aProtein Internet Molecular Sequence Data Protein Conformation Proteins/*chemistry/classification/*metabolism Pseudomonas aeruginosa/*metabolism Sequence Alignment/*methods Sequence Analysis10aProtein/*methods Sequence Homology10aStatistical *Databases1 aMarti-Renom, M., A.1 aPieper, U.1 aMadhusudhan, M., S.1 aRossi, A.1 aEswar, N.1 aDavis, F., P.1 aAl-Shahrour, Fatima1 aDopazo, J.1 aSali, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478513