{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:26:12Z","timestamp":1760707572028},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and\/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We describe a method for the function-related annotation of protein structures by means of the detection of local structural similarity with a library of annotated functional sites. An automatic procedure was used to annotate the function of local surface regions. Next, we employed a sequence-independent algorithm to compare exhaustively these functional patches with a larger collection of protein surface cavities. After tuning and validating the algorithm on a dataset of well annotated structures, we applied it to a list of protein structures that are classified as being of unknown function in the Protein Data Bank. By this strategy, we were able to provide functional clues to proteins that do not show any significant sequence or global structural similarity with proteins in the current databases.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This method is able to spot structural similarities associated to function-related similarities, independently on sequence or fold resemblance, therefore is a valuable tool for the functional analysis of uncharacterized proteins. Results are available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/cbm.bio.uniroma2.it\/surface\/structuralGenomics.html\">http:\/\/cbm.bio.uniroma2.it\/surface\/structuralGenomics.html<\/jats:ext-link><\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-194","type":"journal-article","created":{"date-parts":[[2005,8,3]],"date-time":"2005-08-03T06:14:17Z","timestamp":1123049657000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Functional annotation by identification of local surface similarities: a novel tool for structural genomics"],"prefix":"10.1186","volume":"6","author":[{"given":"Fabrizio","family":"Ferr\u00e8","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Ausiello","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Zanzoni","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuela","family":"Helmer-Citterich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,8,2]]},"reference":[{"issue":"1","key":"519_CR1","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/S0958-1669(99)00064-6","volume":"11","author":"L Shapiro","year":"2000","unstructured":"Shapiro L, Harris T: Finding function through structural genomics. Curr Opin Biotechnol 2000, 11(1):31\u201335. 10.1016\/S0958-1669(99)00064-6","journal-title":"Curr Opin Biotechnol"},{"issue":"3","key":"519_CR2","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1017\/S0033583503003901","volume":"36","author":"JC Whisstock","year":"2003","unstructured":"Whisstock JC, Lesk AM: Prediction of protein function from protein sequence and structure. Q Rev Biophys 2003, 36(3):307\u2013340. 10.1017\/S0033583503003901","journal-title":"Q Rev Biophys"},{"issue":"3","key":"519_CR3","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1002\/prot.340160306","volume":"16","author":"D Fischer","year":"1993","unstructured":"Fischer D, Norel R, Wolfson H, Nussinov R: Surface motifs by a computer vision technique: searches, detection, and implications for protein-ligand recognition. Proteins 1993, 16(3):278\u2013292. 10.1002\/prot.340160306","journal-title":"Proteins"},{"issue":"1","key":"519_CR4","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1093\/protein\/7.1.39","volume":"7","author":"R Norel","year":"1994","unstructured":"Norel R, Fischer D, Wolfson HJ, Nussinov R: Molecular surface recognition by a computer vision-based technique. Protein Eng 1994, 7(1):39\u201346.","journal-title":"Protein Eng"},{"issue":"4","key":"519_CR5","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1016\/S0958-1669(98)80013-X","volume":"9","author":"LM Kauvar","year":"1998","unstructured":"Kauvar LM, Villar HO: Deciphering cryptic similarities in protein binding sites. Curr Opin Biotechnol 1998, 9(4):390\u2013394. 10.1016\/S0958-1669(98)80013-X","journal-title":"Curr Opin Biotechnol"},{"issue":"3","key":"519_CR6","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1006\/jmbi.1996.0264","volume":"258","author":"AM Lesk","year":"1996","unstructured":"Lesk AM, Fordham WD: Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J Mol Biol 1996, 258(3):501\u2013537. 10.1006\/jmbi.1996.0264","journal-title":"J Mol Biol"},{"issue":"5","key":"519_CR7","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1002\/pro.5560030506","volume":"3","author":"D Fischer","year":"1994","unstructured":"Fischer D, Wolfson H, Lin SL, Nussinov R: Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci 1994, 3(5):769\u2013778.","journal-title":"Protein Sci"},{"issue":"49","key":"519_CR8","doi-asserted-by":"publisher","first-page":"31426","DOI":"10.1074\/jbc.271.49.31426","volume":"271","author":"JA Contreras","year":"1996","unstructured":"Contreras JA, Karlsson M, Osterlund T, Laurell H, Svensson A, Holm C: Hormone-sensitive lipase is structurally related to acetylcholinesterase, bile salt-stimulated lipase, and several fungal lipases. Building of a three-dimensional model for the catalytic domain of hormone-sensitive lipase. J Biol Chem 1996, 271(49):31426\u201331430. 10.1074\/jbc.271.49.31426","journal-title":"J Biol Chem"},{"issue":"1","key":"519_CR9","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/nsb0197-6","volume":"4","author":"N Kobayashi","year":"1997","unstructured":"Kobayashi N, Go N: ATP binding proteins with different folds share a common ATP-binding structural motif. Nat Struct Biol 1997, 4(1):6\u20137. 10.1038\/nsb0197-6","journal-title":"Nat Struct Biol"},{"issue":"4","key":"519_CR10","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1006\/jmbi.2000.4151","volume":"303","author":"A Via","year":"2000","unstructured":"Via A, Ferre F, Brannetti B, Valencia A, Helmer-Citterich M: Three-dimensional view of the surface motif associated with the P-loop structure: cis and trans cases of convergent evolution. J Mol Biol 2000, 303(4):455\u2013465. 10.1006\/jmbi.2000.4151","journal-title":"J Mol Biol"},{"issue":"7","key":"519_CR11","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1038\/10745","volume":"6","author":"KY Hwang","year":"1999","unstructured":"Hwang KY, Chung JH, Kim SH, Han YS, Cho Y: Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat Struct Biol 1999, 6(7):691\u2013696. 10.1038\/10745","journal-title":"Nat Struct Biol"},{"issue":"4808","key":"519_CR12","doi-asserted-by":"publisher","first-page":"1554","DOI":"10.1126\/science.3589669","volume":"236","author":"G Wistow","year":"1987","unstructured":"Wistow G, Piatigorsky J: Recruitment of enzymes as lens structural proteins. Science 1987, 236(4808):1554\u20131556.","journal-title":"Science"},{"issue":"1","key":"519_CR13","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1002\/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L","volume":"28","author":"L Holm","year":"1997","unstructured":"Holm L, Sander C: An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 1997, 28(1):72\u201382. 10.1002\/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L","journal-title":"Proteins"},{"issue":"5","key":"519_CR14","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1002\/(SICI)1521-1878(199905)21:5<432::AID-BIES10>3.0.CO;2-T","volume":"21","author":"MD Ganfornina","year":"1999","unstructured":"Ganfornina MD, Sanchez D: Generation of evolutionary novelty by functional shift. Bioessays 1999, 21(5):432\u2013439. 10.1002\/(SICI)1521-1878(199905)21:5<432::AID-BIES10>3.0.CO;2-T","journal-title":"Bioessays"},{"issue":"8","key":"519_CR15","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/S0968-0004(02)02158-8","volume":"27","author":"AE Todd","year":"2002","unstructured":"Todd AE, Orengo CA, Thornton JM: Plasticity of enzyme active sites. Trends Biochem Sci 2002, 27(8):419\u2013426. 10.1016\/S0968-0004(02)02158-8","journal-title":"Trends Biochem Sci"},{"issue":"12","key":"519_CR16","first-page":"2438","volume":"5","author":"RA Laskowski","year":"1996","unstructured":"Laskowski RA, Luscombe NM, Swindells MB, Thornton JM: Protein clefts in molecular recognition and function. Protein Sci 1996, 5(12):2438\u20132452.","journal-title":"Protein Sci"},{"issue":"4","key":"519_CR17","doi-asserted-by":"publisher","first-page":"1887","DOI":"10.1006\/jmbi.1998.2393","volume":"285","author":"GJ Kleywegt","year":"1999","unstructured":"Kleywegt GJ: Recognition of spatial motifs in protein structures. J Mol Biol 1999, 285(4):1887\u20131897. 10.1006\/jmbi.1998.2393","journal-title":"J Mol Biol"},{"issue":"4","key":"519_CR18","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/protein\/11.4.263","volume":"11","author":"M Rosen","year":"1998","unstructured":"Rosen M, Lin SL, Wolfson H, Nussinov R: Molecular shape comparisons in searches for active sites and functional similarity. Protein Eng 1998, 11(4):263\u2013277. 10.1093\/protein\/11.4.263","journal-title":"Protein Eng"},{"issue":"9","key":"519_CR19","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1023\/A:1013158818807","volume":"15","author":"R Preissner","year":"2001","unstructured":"Preissner R, Goede A, Rother K, Osterkamp F, Koert U, Froemmel C: Matching organic libraries with protein-substructures. J Comput Aided Mol Des 2001, 15(9):811\u2013817. 10.1023\/A:1013158818807","journal-title":"J Comput Aided Mol Des"},{"issue":"8","key":"519_CR20","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1110\/ps.0368703","volume":"12","author":"K Kinoshita","year":"2003","unstructured":"Kinoshita K, Nakamura H: Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 2003, 12(8):1589\u20131595. 10.1110\/ps.0368703","journal-title":"Protein Sci"},{"issue":"2","key":"519_CR21","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/S0022-2836(02)00811-2","volume":"323","author":"S Schmitt","year":"2002","unstructured":"Schmitt S, Kuhn D, Klebe G: A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 2002, 323(2):387\u2013406. 10.1016\/S0022-2836(02)00811-2","journal-title":"J Mol Biol"},{"issue":"2","key":"519_CR22","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/S0022-2836(03)00882-9","volume":"332","author":"TA Binkowski","year":"2003","unstructured":"Binkowski TA, Adamian L, Liang J: Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol 2003, 332(2):505\u2013526. 10.1016\/S0022-2836(03)00882-9","journal-title":"J Mol Biol"},{"issue":"5","key":"519_CR23","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1016\/S0022-2836(03)00045-7","volume":"326","author":"A Stark","year":"2003","unstructured":"Stark A, Sunyaev S, Russell RB: A model for statistical significance of local similarities in structure. J Mol Biol 2003, 326(5):1307\u20131316. 10.1016\/S0022-2836(03)00045-7","journal-title":"J Mol Biol"},{"issue":"13","key":"519_CR24","doi-asserted-by":"publisher","first-page":"3341","DOI":"10.1093\/nar\/gkg506","volume":"31","author":"A Stark","year":"2003","unstructured":"Stark A, Russell RB: Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 2003, 31(13):3341\u20133344. 10.1093\/nar\/gkg506","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"519_CR25","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.1016\/j.str.2004.05.012","volume":"12","author":"A Stark","year":"2004","unstructured":"Stark A, Shkumatov A, Russell RB: Finding functional sites in structural genomics proteins. Structure (Camb) 2004, 12(8):1405\u20131412. 10.1016\/j.str.2004.05.012","journal-title":"Structure (Camb)"},{"key":"519_CR26","first-page":"228","volume-title":"Pac Symp Biocomput","author":"R Singh","year":"2003","unstructured":"Singh R, Saha M: Identifying structural motifs in proteins. Pac Symp Biocomput 2003, 228\u2013239."},{"key":"519_CR27","first-page":"334","volume-title":"Pac Symp Biocomput","author":"BY Chen","year":"2005","unstructured":"Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE: Algorithms for structural comparison and statistical analysis of 3D protein motifs. Pac Symp Biocomput 2005, 334\u2013345."},{"issue":"9","key":"519_CR28","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1093\/bioinformatics\/bth083","volume":"20","author":"M Schmollinger","year":"2004","unstructured":"Schmollinger M, Fischer I, Nerz C, Pinkenburg S, Gotz F, Kaufmann M, Lange KJ, Reuter R, Rosenstiel W, Zell A: ParSeq: searching motifs with structural and biochemical properties. Bioinformatics 2004, 20(9):1459\u20131461. 10.1093\/bioinformatics\/bth083","journal-title":"Bioinformatics"},{"issue":"3","key":"519_CR29","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/j.jmb.2005.01.044","volume":"347","author":"JW Torrance","year":"2005","unstructured":"Torrance JW, Bartlett GJ, Porter CT, Thornton JM: Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 2005, 347(3):565\u2013581. 10.1016\/j.jmb.2005.01.044","journal-title":"J Mol Biol"},{"issue":"3","key":"519_CR30","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1016\/S0022-2836(02)01384-0","volume":"326","author":"PP Wangikar","year":"2003","unstructured":"Wangikar PP, Tendulkar AV, Ramya S, Mali DN, Sarawagi S: Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol 2003, 326(3):955\u2013978. 10.1016\/S0022-2836(02)01384-0","journal-title":"J Mol Biol"},{"issue":"1","key":"519_CR31","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.str.2004.10.015","volume":"13","author":"D Pal","year":"2005","unstructured":"Pal D, Eisenberg D: Inference of protein function from protein structure. Structure (Camb) 2005, 13(1):121\u2013130. 10.1016\/j.str.2004.10.015","journal-title":"Structure (Camb)"},{"issue":"Database","key":"519_CR32","doi-asserted-by":"publisher","first-page":"D240","DOI":"10.1093\/nar\/gkh054","volume":"32","author":"F Ferre","year":"2004","unstructured":"Ferre F, Ausiello G, Zanzoni A, Helmer-Citterich M: SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res 2004, 32(Database):D240\u2013244. 10.1093\/nar\/gkh054","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"519_CR33","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/30.1.235","volume":"30","author":"L Falquet","year":"2002","unstructured":"Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A: The PROSITE database, its status in 2002. Nucleic Acids Res 2002, 30(1):235\u2013238. 10.1093\/nar\/30.1.235","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"519_CR34","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1093\/nar\/gkg545","volume":"31","author":"P Puntervoll","year":"2003","unstructured":"Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, et al.: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 2003, 31(13):3625\u20133630. 10.1093\/nar\/gkg545","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"519_CR35","doi-asserted-by":"publisher","first-page":"D262","DOI":"10.1093\/nar\/gkh021","volume":"32","author":"E Camon","year":"2004","unstructured":"Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, 32(Database):D262\u2013266. 10.1093\/nar\/gkh021","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"519_CR36","doi-asserted-by":"publisher","first-page":"1700","DOI":"10.1002\/pro.5560070805","volume":"7","author":"IL Alberts","year":"1998","unstructured":"Alberts IL, Nadassy K, Wodak SJ: Analysis of zinc binding sites in protein crystal structures. Protein Sci 1998, 7(8):1700\u20131716.","journal-title":"Protein Sci"},{"issue":"4","key":"519_CR37","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1016\/0958-1669(92)90166-G","volume":"3","author":"JA Tainer","year":"1992","unstructured":"Tainer JA, Roberts VA, Getzoff ED: Protein metal-binding sites. Curr Opin Biotechnol 1992, 3(4):378\u2013387. 10.1016\/0958-1669(92)90166-G","journal-title":"Curr Opin Biotechnol"},{"issue":"6","key":"519_CR38","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1016\/j.sbi.2004.10.012","volume":"14","author":"DP Barondeau","year":"2004","unstructured":"Barondeau DP, Getzoff ED: Structural insights into protein-metal ion partnerships. Curr Opin Struct Biol 2004, 14(6):765\u2013774. 10.1016\/j.sbi.2004.10.012","journal-title":"Curr Opin Struct Biol"},{"issue":"Database","key":"519_CR39","doi-asserted-by":"publisher","first-page":"D226","DOI":"10.1093\/nar\/gkh039","volume":"32","author":"A Andreeva","year":"2004","unstructured":"Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 2004, 32(Database):D226\u2013229. 10.1093\/nar\/gkh039","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"519_CR40","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/S0969-2126(01)00622-0","volume":"9","author":"AA McCarthy","year":"2001","unstructured":"McCarthy AA, Baker HM, Shewry SC, Patchett ML, Baker EN: Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold. Structure (Camb) 2001, 9(7):637\u2013646. 10.1016\/S0969-2126(01)00622-0","journal-title":"Structure (Camb)"},{"issue":"3","key":"519_CR41","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1016\/S0968-0004(99)01533-9","volume":"25","author":"MW Fraaije","year":"2000","unstructured":"Fraaije MW, Mattevi A: Flavoenzymes: diverse catalysts with recurrent features. Trends Biochem Sci 2000, 25(3):126\u2013132. 10.1016\/S0968-0004(99)01533-9","journal-title":"Trends Biochem Sci"},{"issue":"9","key":"519_CR42","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.1110\/ps.12801","volume":"10","author":"O Dym","year":"2001","unstructured":"Dym O, Eisenberg D: Sequence-structure analysis of FAD-containing proteins. Protein Sci 2001, 10(9):1712\u20131728. 10.1110\/ps.12801","journal-title":"Protein Sci"},{"issue":"2","key":"519_CR43","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1111\/j.1574-6968.1999.tb13575.x","volume":"174","author":"TA Tatusova","year":"1999","unstructured":"Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174(2):247\u2013250. 10.1016\/S0378-1097(99)00149-4","journal-title":"FEMS Microbiol Lett"},{"key":"519_CR44","volume-title":"Proceedings of the 5th International Conference on Molecular Structural Biology, Vienna, September 3\u20137 2003","author":"E Krissinel","year":"2003","unstructured":"Krissinel E, Henrick K: Protein structure comparison in 3D based on secondary structure matching (SSM) followed by Ca alignment, scored by a new structural similarity function. Proceedings of the 5th International Conference on Molecular Structural Biology, Vienna, September 3\u20137 2003 2003., 88:"},{"issue":"3","key":"519_CR45","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1016\/S0959-440X(00)00215-3","volume":"11","author":"SA Teichmann","year":"2001","unstructured":"Teichmann SA, Murzin AG, Chothia C: Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol 2001, 11(3):354\u2013363. 10.1016\/S0959-440X(00)00215-3","journal-title":"Curr Opin Struct Biol"},{"issue":"4","key":"519_CR46","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1110\/ps.4570102","volume":"11","author":"MR Chance","year":"2002","unstructured":"Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, et al.: Structural genomics: a pipeline for providing structures for the biologist. Protein Sci 2002, 11(4):723\u2013738. 10.1110\/ps.4570102","journal-title":"Protein Sci"},{"issue":"5","key":"519_CR47","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1016\/S1367-5931(99)00007-1","volume":"3","author":"AE Todd","year":"1999","unstructured":"Todd AE, Orengo CA, Thornton JM: Evolution of protein function, from a structural perspective. Curr Opin Chem Biol 1999, 3(5):548\u2013556. 10.1016\/S1367-5931(99)00007-1","journal-title":"Curr Opin Chem Biol"},{"issue":"Suppl","key":"519_CR48","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/80784","volume":"7","author":"JM Thornton","year":"2000","unstructured":"Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA: From structure to function: approaches and limitations. Nat Struct Biol 2000, 7(Suppl):991\u2013994. 10.1038\/80784","journal-title":"Nat Struct Biol"},{"issue":"3","key":"519_CR49","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1002\/1097-0134(20010215)42:3<378::AID-PROT70>3.0.CO;2-3","volume":"42","author":"JA Irving","year":"2001","unstructured":"Irving JA, Whisstock JC, Lesk AM: Protein structural alignments and functional genomics. Proteins 2001, 42(3):378\u2013382. 10.1002\/1097-0134(20010215)42:3<378::AID-PROT70>3.0.CO;2-3","journal-title":"Proteins"},{"issue":"Web server issu","key":"519_CR50","doi-asserted-by":"publisher","first-page":"W133","DOI":"10.1093\/nar\/gki499","volume":"33","author":"G Ausiello","year":"2005","unstructured":"Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M: pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Research 2005, 33(Web server issue):W133\u20137. 10.1093\/nar\/gki499","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"519_CR51","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/0263-7855(95)00073-9","volume":"13","author":"RA Laskowski","year":"1995","unstructured":"Laskowski RA: SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13(5):323\u2013330. 307\u2013328 10.1016\/0263-7855(95)00073-9","journal-title":"J Mol Graph"},{"issue":"Pt 6 No 1","key":"519_CR52","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1107\/S0907444902003451","volume":"58","author":"HM Berman","year":"2002","unstructured":"Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, et al.: The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002, 58(Pt 6 No 1):899\u2013907. 10.1107\/S0907444902003451","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"10","key":"519_CR53","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1002\/1615-9861(200210)2:10<1435::AID-PROT1435>3.0.CO;2-9","volume":"2","author":"A Gattiker","year":"2002","unstructured":"Gattiker A, Bienvenut WV, Bairoch A, Gasteiger E: FindPept, a tool to identify unmatched masses in peptide mass fingerprinting protein identification. Proteomics 2002, 2(10):1435\u20131444. 10.1002\/1615-9861(200210)2:10<1435::AID-PROT1435>3.0.CO;2-9","journal-title":"Proteomics"},{"key":"519_CR54","volume-title":"Department of Biochemistry and Molecular Biology","author":"S Hubbard","year":"1993","unstructured":"Hubbard S, Thornton JM: NACCESS, Computer Program. In Department of Biochemistry and Molecular Biology. University College London; 1993."},{"issue":"2","key":"519_CR55","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/0022-2836(91)90027-4","volume":"220","author":"SJ Hubbard","year":"1991","unstructured":"Hubbard SJ, Campbell SF, Thornton JM: Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 1991, 220(2):507\u2013530. 10.1016\/0022-2836(91)90027-4","journal-title":"J Mol Biol"},{"issue":"15","key":"519_CR56","doi-asserted-by":"publisher","first-page":"1849","DOI":"10.1002\/jcc.20110","volume":"25","author":"EA Coutsias","year":"2004","unstructured":"Coutsias EA, Seok C, Dill KA: Using quaternions to calculate RMSD. J Comput Chem 2004, 25(15):1849\u20131857. 10.1002\/jcc.20110","journal-title":"J Comput Chem"},{"key":"519_CR57","volume-title":"Matrices for detecting distant relationships","author":"R Schwartz","year":"1979","unstructured":"Schwartz R, Dayhoff M: Matrices for detecting distant relationships. Foundation NBR. Washington DC; 1979."},{"issue":"1","key":"519_CR58","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31(1):365\u2013370. 10.1093\/nar\/gkg095","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"519_CR59","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276\u2013277. 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends Genet"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-194.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T17:48:30Z","timestamp":1706809710000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-194"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,8,2]]},"references-count":59,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["519"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-194","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,8,2]]},"assertion":[{"value":"26 January 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 August 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 August 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"194"}}