{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:17:00Z","timestamp":1775873820131,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design.<\/jats:p>\n               <jats:p>Results: We propose a novel graph-based\u2013binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor\u2019s techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario.<\/jats:p>\n               <jats:p>Availability and implementation: Datasets and the source code are available at http:\/\/www.dcc.ufmg.br\/\u223cdpires\/acsm.<\/jats:p>\n               <jats:p>Contact: \u00a0dpires@dcc.ufmg.br or raquelcm@dcc.ufmg.br<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt058","type":"journal-article","created":{"date-parts":[[2013,2,10]],"date-time":"2013-02-10T01:09:00Z","timestamp":1360458540000},"page":"855-861","source":"Crossref","is-referenced-by-count":62,"title":["aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction"],"prefix":"10.1093","volume":"29","author":[{"given":"Douglas E. V.","family":"Pires","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"},{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"}]},{"given":"Raquel C.","family":"de Melo-Minardi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"}]},{"given":"Carlos H.","family":"da Silveira","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"}]},{"given":"Frederico F.","family":"Campos","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"}]},{"suffix":"Jr","given":"Wagner","family":"Meira","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Ant\u00f4nio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1, Rua Irm\u00e3 Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2013,2,8]]},"reference":[{"key":"2023020303304869200_btt058-B1","doi-asserted-by":"crossref","first-page":"e740","DOI":"10.1371\/journal.pntd.0000740","article-title":"In vitro and in vivo high-throughput assays for the testing of anti-trypanosoma cruzi compounds","volume":"4","author":"Canavaci","year":"2010","journal-title":"PLoS Negl. Trop. Dis."},{"key":"2023020303304869200_btt058-B2","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1002\/prot.22187","article-title":"Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins","volume":"74","author":"da Silveira","year":"2009","journal-title":"Proteins"},{"key":"2023020303304869200_btt058-B3","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1093\/bioinformatics\/btm470","article-title":"The Poisson Index: a new probabilistic model for protein ligand binding site similarity","volume":"23","author":"Davies","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020303304869200_btt058-B4","doi-asserted-by":"crossref","DOI":"10.1137\/1.9781611971446","volume-title":"Applied Numerical Linear Algebra","author":"Demmel","year":"1997"},{"key":"2023020303304869200_btt058-B5","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1093\/bioinformatics\/btr680","article-title":"HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids","volume":"28","author":"Gon\u00e7alves-Almeida","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020303304869200_btt058-B6","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/1471-2105-11-99","article-title":"A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction","volume":"11","author":"Hoffmann","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023020303304869200_btt058-B7","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.jmb.2007.01.086","article-title":"Shape variation in protein binding pockets and their ligands","volume":"368","author":"Kahraman","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2023020303304869200_btt058-B8","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1016\/j.jmb.2006.01.072","article-title":"Surprisingly high correlation between early and late stages in non-two-state protein folding","volume":"357","author":"Kamagata","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023020303304869200_btt058-B9","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1002\/prot.22639","article-title":"Detection of multiscale pockets on protein surfaces using mathematical morphology","volume":"78","author":"Kawabata","year":"2010","journal-title":"Proteins"},{"key":"2023020303304869200_btt058-B10","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.44.2.98","article-title":"Application of a theory of enzyme specificity to protein synthesis","volume":"44","author":"Koshland","year":"1958","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303304869200_btt058-B11","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-10-168","article-title":"Fpocket: an open source platform for ligand pocket detection","volume":"10","author":"Le Guilloux","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020303304869200_btt058-B12","doi-asserted-by":"crossref","first-page":"e916","DOI":"10.1371\/journal.pntd.0000916","article-title":"The potential economic value of a trypanosoma cruzi (chagas disease) vaccine in latin america","volume":"4","author":"Lee","year":"2010","journal-title":"PLoS Negl. Trop. Dis."},{"key":"2023020303304869200_btt058-B13","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/S0022-2836(63)80091-1","article-title":"Allosteric proteins and cellular control systems","volume":"6","author":"Monod","year":"1963","journal-title":"J. Mol. Biol."},{"key":"2023020303304869200_btt058-B14","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1093\/bioinformatics\/bti337","article-title":"Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons","volume":"21","author":"Morris","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020303304869200_btt058-B15","doi-asserted-by":"crossref","first-page":"i105","DOI":"10.1093\/bioinformatics\/btn263","article-title":"Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites","volume":"24","author":"Najmanovich","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020303304869200_btt058-B16","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2164-12-S4-S12","article-title":"Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns","volume":"12","author":"Pires","year":"2011","journal-title":"BMC Genomics"},{"key":"2023020303304869200_btt058-B17","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/S0140-6736(10)60061-X","article-title":"Chagas disease","volume":"375","author":"Rassi","year":"2010","journal-title":"Lancet"},{"key":"2023020303304869200_btt058-B18","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1002\/prot.21858","article-title":"A simple and fuzzy method to align and compare druggable ligand-binding sites","volume":"71","author":"Schalon","year":"2008","journal-title":"Proteins"},{"issue":"web server issue","key":"2023020303304869200_btt058-B19","doi-asserted-by":"crossref","first-page":"W260","DOI":"10.1093\/nar\/gkn185","article-title":"MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions","volume":"36","author":"Shulman-Peleg","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023020303304869200_btt058-B20","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1023\/A:1008115913787","article-title":"Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods","volume":"14","author":"Sippl","year":"2000","journal-title":"J. Comput. Aided Mol. Des."},{"key":"2023020303304869200_btt058-B21","doi-asserted-by":"crossref","first-page":"2746","DOI":"10.1002\/prot.23103","article-title":"Surface-based protein binding pocket similarity","volume":"79","author":"Spitzer","year":"2011","journal-title":"Proteins"},{"key":"2023020303304869200_btt058-B22","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1472-6807-12-5","article-title":"Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands","volume":"12","author":"Ueno","year":"2012","journal-title":"BMC Struct. Biol."},{"key":"2023020303304869200_btt058-B23","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1109\/TCBB.2007.358301","article-title":"Multiple graph alignment for the structural analysis of protein active sites","volume":"4","author":"Weskamp","year":"2007","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"2023020303304869200_btt058-B24","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1006\/jmbi.1996.0859","article-title":"Determination of atomic desolvation energies from the structures of crystallized proteins","volume":"267","author":"Zhang","year":"1997","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/7\/855\/49060831\/bioinformatics_29_7_855.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/7\/855\/49060831\/bioinformatics_29_7_855.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T03:31:54Z","timestamp":1675395114000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/7\/855\/253252"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,2,8]]},"references-count":24,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2013,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt058","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,4,1]]},"published":{"date-parts":[[2013,2,8]]}}}