{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T02:58:15Z","timestamp":1777431495248,"version":"3.51.4"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Council of Brazil","award":["308124\/2015-4"],"award-info":[{"award-number":["308124\/2015-4"]}]},{"DOI":"10.13039\/501100004263","name":"FAPERGS","doi-asserted-by":"crossref","award":["TO2054-2551\/13-0"],"award-info":[{"award-number":["TO2054-2551\/13-0"]}],"id":[{"id":"10.13039\/501100004263","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004263","name":"FAPERGS","doi-asserted-by":"crossref","award":["2304-2551\/14"],"award-info":[{"award-number":["2304-2551\/14"]}],"id":[{"id":"10.13039\/501100004263","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2222-2","type":"journal-article","created":{"date-parts":[[2018,6,21]],"date-time":"2018-06-21T22:15:16Z","timestamp":1529619316000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["A selective method for optimizing ensemble docking-based experiments on an InhA Fully-Flexible receptor model"],"prefix":"10.1186","volume":"19","author":[{"given":"Renata","family":"De Paris","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Vahl Quevedo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4071-3246","authenticated-orcid":false,"given":"Duncan D.","family":"Ruiz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Furia","family":"Gargano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osmar Norberto","family":"de Souza","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,6,22]]},"reference":[{"issue":"8","key":"2222_CR1","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/nrd4336","volume":"13","author":"J Eder","year":"2014","unstructured":"Eder J, Sedrani R, Wiesmann C. The discovery of first-in-class drugs: origins and evolution. Nat Rev Drug Discov. 2014; 13(8):577.","journal-title":"Nat Rev Drug Discov"},{"issue":"1","key":"2222_CR2","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.ejphar.2009.06.065","volume":"625","author":"S Mandal","year":"2009","unstructured":"Mandal S, Moudgil M, Mandal SK. Rational drug design. Eur J Pharmacol. 2009; 625(1):90\u2013100.","journal-title":"Eur J Pharmacol"},{"issue":"3","key":"2222_CR3","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/nrd3078","volume":"9","author":"SM Paul","year":"2010","unstructured":"Paul SM, Mytelka DS, Dunwiddie CT, Persinger CC, Munos BH, Lindborg SR, Schacht AL. How to improve r&d productivity: the pharmaceutical industry\u2019s grand challenge. Nat Rev Drug Discov. 2010; 9(3):203\u201314.","journal-title":"Nat Rev Drug Discov"},{"issue":"5073","key":"2222_CR4","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1126\/science.257.5073.1078","volume":"257","author":"ID Kuntz","year":"1992","unstructured":"Kuntz ID. Structure-Based Strategies for Drug Design and Discovery. Science. 1992; 257(5073):1078\u201382.","journal-title":"Science"},{"issue":"2","key":"2222_CR5","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/j.cbi.2006.12.006","volume":"171","author":"I Kapetanovic","year":"2008","unstructured":"Kapetanovic I. Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach. Chem Biol Interact. 2008; 171(2):165\u201376.","journal-title":"Chem Biol Interact"},{"issue":"2","key":"2222_CR6","doi-asserted-by":"publisher","first-page":"146","DOI":"10.2174\/157340911795677602","volume":"7","author":"X-Y Meng","year":"2011","unstructured":"Meng X-Y, Zhang H-X, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011; 7(2):146\u201357.","journal-title":"Curr Comput Aided Drug Des"},{"issue":"9","key":"2222_CR7","doi-asserted-by":"publisher","first-page":"1217","DOI":"10.2174\/138161212799436386","volume":"18","author":"L Chen","year":"2012","unstructured":"Chen L, K Morrow J, T Tran H, S Phatak S, Du-Cuny L, Zhang S. From laptop to benchtop to bedside: structure-based drug design on protein targets. Curr Pharm Des. 2012; 18(9):1217\u201339.","journal-title":"Curr Pharm Des"},{"issue":"16","key":"2222_CR8","doi-asserted-by":"publisher","first-page":"2785","DOI":"10.1002\/jcc.21256","volume":"30","author":"GM Morris","year":"2009","unstructured":"Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009; 30(16):2785\u201391.","journal-title":"J Comput Chem"},{"issue":"5","key":"2222_CR9","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/nprot.2016.051","volume":"11","author":"S Forli","year":"2016","unstructured":"Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein\u2013ligand docking and virtual drug screening with the autodock suite. Nat Protoc. 2016; 11(5):905.","journal-title":"Nat Protoc"},{"issue":"6","key":"2222_CR10","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1261\/rna.1563609","volume":"15","author":"PT Lang","year":"2009","unstructured":"Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. DOCK 6: Combining techniques to model RNA\u2013small molecule complexes. RNA. 2009; 15(6):1219\u201330.","journal-title":"RNA"},{"issue":"18","key":"2222_CR11","doi-asserted-by":"publisher","first-page":"2296","DOI":"10.2174\/0929867311320180002","volume":"20","author":"S Sousa","year":"2013","unstructured":"Sousa S, Ribeiro A, Coimbra J, Neves R, Martins S, Moorthy N, Fernandes P, Ramos M. Protein-ligand docking in the new millennium\u2013a retrospective of 10 years in the field. Curr Med Chem. 2013; 20(18):2296\u2013314.","journal-title":"Curr Med Chem"},{"issue":"7","key":"2222_CR12","first-page":"1141","volume":"10","author":"R Buonfiglio","year":"2015","unstructured":"Buonfiglio R, Recanatini M, Masetti M. Protein flexibility in drug discovery: From theory to computation. ChemMedChem - Chem Enabling Drug Disc. 2015; 10(7):1141\u20138.","journal-title":"ChemMedChem - Chem Enabling Drug Disc"},{"key":"2222_CR13","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.bpc.2013.10.007","volume":"186","author":"F Feixas","year":"2014","unstructured":"Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014; 186:31\u201345.","journal-title":"Biophys Chem"},{"issue":"5","key":"2222_CR14","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1002\/med.20067","volume":"26","author":"H Alonso","year":"2006","unstructured":"Alonso H, Bliznyuk AA, Gready JE. Combining docking and molecular dynamic simulations in drug design. Med Res Rev. 2006; 26(5):531\u201368.","journal-title":"Med Res Rev"},{"issue":"20","key":"2222_CR15","doi-asserted-by":"publisher","first-page":"6237","DOI":"10.1021\/jm800562d","volume":"51","author":"P Cozzini","year":"2008","unstructured":"Cozzini P, Kellogg GE, Spyrakis F, Abraham DJ, Costantino G, Emerson A, Fanelli F, Gohlke H, Kuhn LA, Morris GM, Orozco M, Pertinhez TA, Rizzi M, Sotriffer CA. Target flexibility: An emerging consideration in drug discovery and design. Eur J Med Chem. 2008; 51(20):6237\u201355.","journal-title":"Eur J Med Chem"},{"issue":"6","key":"2222_CR16","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1002\/widm.46","volume":"1","author":"KS Machado","year":"2011","unstructured":"Machado KS, Winck AT, Ruiz DD, Norberto de Souza O. Mining flexible-receptor molecular docking data. Wiley Interdisc Rev Data Min Knowl Disc. 2011; 1(6):532\u201341.","journal-title":"Wiley Interdisc Rev Data Min Knowl Disc"},{"issue":"9","key":"2222_CR17","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1007\/s10822-007-9159-2","volume":"22","author":"RE Amaro","year":"2008","unstructured":"Amaro RE, Baron R, McCammon JA. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des. 2008; 22(9):693\u2013705.","journal-title":"J Comput Aided Mol Des"},{"key":"2222_CR18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2013\/469363","volume":"2013","author":"R De Paris","year":"2013","unstructured":"De Paris R, Frantz FA, Norberto de Souza O, Ruiz DD. wFReDoW: A cloud-based web environment to handle molecular docking simulations of a fully flexible receptor model. BioMed Res Int. 2013; 2013:1\u201312.","journal-title":"BioMed Res Int"},{"issue":"16","key":"2222_CR19","doi-asserted-by":"publisher","first-page":"7608","DOI":"10.1016\/j.eswa.2014.05.038","volume":"41","author":"CV Quevedo","year":"2014","unstructured":"Quevedo CV, De Paris R, Ruiz DD, Norberto de Souza O. A strategic solution to optimize molecular docking simulations using fully-flexible receptor models. Expert Syst Appl. 2014; 41(16):7608\u201320.","journal-title":"Expert Syst Appl"},{"issue":"7","key":"2222_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0133172","volume":"10","author":"R De Paris","year":"2015","unstructured":"De Paris R, Quevedo CV, Ruiz DD, Noberto de Souza O. An effective approach for clustering InhA molecular dynamics trajectory using substrate-binding cavity features. PloS ONE. 2015; 10(7):1\u201325.","journal-title":"PloS ONE"},{"issue":"12","key":"2222_CR21","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1517\/17460441.2015.1094458","volume":"10","author":"DA Antunes","year":"2015","unstructured":"Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Disc. 2015; 10(12):1301\u201313.","journal-title":"Expert Opin Drug Disc"},{"issue":"6","key":"2222_CR22","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1002\/jcc.21696","volume":"32","author":"B Collignon","year":"2011","unstructured":"Collignon B, Schulz R, Smith JC, Baudry J. Task-parallel message passing interface implementation of autodock4 for docking of very large databases of compounds using high-performance super-computers. J Comput Chem. 2011; 32(6):1202\u20139.","journal-title":"J Comput Chem"},{"issue":"11","key":"2222_CR23","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1002\/jcc.23214","volume":"34","author":"X Zhang","year":"2013","unstructured":"Zhang X, Wong SE, Lightstone FC. Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines. J Comput Chem. 2013; 34(11):915\u201327.","journal-title":"J Comput Chem"},{"key":"2222_CR24","volume-title":"The Grid 2: Blueprint for a New Computing Infrastructure","author":"I Foster","year":"2003","unstructured":"Foster I, Kesselman C. The Grid 2: Blueprint for a New Computing Infrastructure. San Francisco: Morgan Kaufmann; 2003."},{"issue":"10","key":"2222_CR25","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1002\/cpe.3113","volume":"26","author":"T Kiss","year":"2014","unstructured":"Kiss T, Borsody P, Terstyanszky G, Winter S, Greenwell P, McEldowney S, Heindl H. Large-scale virtual screening experiments on Windows Azure-based cloud resources. Concurr Comput: Pract Experience. 2014; 26(10):1760\u201370.","journal-title":"Concurr Comput: Pract Experience"},{"issue":"1","key":"2222_CR26","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1002\/cpe.2926","volume":"26","author":"SR Ellingson","year":"2014","unstructured":"Ellingson SR, Baudry J. High-throughput virtual molecular docking with AutoDockCloud. Concurr Comput: Pract Experience. 2014; 26(1):907\u201316.","journal-title":"Concurr Comput: Pract Experience"},{"key":"2222_CR27","volume-title":"IEEE International Parallel & Distributed Processing Symposium Workshops","author":"K Oca\u00f1a","year":"2014","unstructured":"Oca\u00f1a K, Benza S, De Oliveira D, Dias J, Mattoso M. Exploring large scale receptor-ligand pairs in molecular docking workflows in HPC clouds. In: IEEE International Parallel & Distributed Processing Symposium Workshops. Washington DC: IEEE Computer Society: 2014. p. 536\u201345."},{"key":"2222_CR28","volume-title":"11th International Conference on e-Science","author":"A Nguyen","year":"2015","unstructured":"Nguyen A, Matsunaga A, Tsugawa M, Ichikawa K, Haga JH, et al. Deployment of a multi-site cloud environment for molecular virtual screenings. In: 11th International Conference on e-Science. Munich: IEEE International Conference on e-Science: 2015. p. 145\u201354."},{"issue":"1","key":"2222_CR29","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13321-017-0204-4","volume":"9","author":"M Capuccini","year":"2017","unstructured":"Capuccini M, Ahmed L, Schaal W, Laure E, Spjuth O. Large-scale virtual screening on public cloud resources with apache spark. J Cheminformatics. 2017; 9(1):15.","journal-title":"J Cheminformatics"},{"issue":"1","key":"2222_CR30","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1529\/biophysj.106.082941","volume":"91","author":"E Lyman","year":"2006","unstructured":"Lyman E, Zuckerman DM. Ensemble-based convergence analysis of biomolecular trajectories. Biophys J. 2006; 91(1):164\u201372.","journal-title":"Biophys J"},{"issue":"2","key":"2222_CR31","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1002\/prot.21214","volume":"66","author":"S-Y Huang","year":"2007","unstructured":"Huang S-Y, Zou X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins Struct Funct Bioinforma. 2007; 66(2):399\u2013421.","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"15","key":"2222_CR32","doi-asserted-by":"publisher","first-page":"4553","DOI":"10.1021\/jm8001668","volume":"51","author":"S Zhong","year":"2008","unstructured":"Zhong S, Chen X, Zhu X, Dziegielewska B, Bachman KE, Ellenberger T, Ballin JD, Wilson GM, Tomkinson AE, MacKerell Jr AD. Identification and validation of human dna ligase inhibitors using computer-aided drug design. J Med Chem. 2008; 51(15):4553\u201362.","journal-title":"J Med Chem"},{"issue":"10","key":"2222_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0048008","volume":"7","author":"S Leis","year":"2012","unstructured":"Leis S, Zacharias M. Reflexin: a flexible receptor protein-ligand docking scheme evaluated on hiv-1 protease. PloS ONE. 2012; 7(10):1\u201313.","journal-title":"PloS ONE"},{"issue":"31","key":"2222_CR34","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.1002\/jcc.23087","volume":"33","author":"J Flick","year":"2012","unstructured":"Flick J, Tristram F, Wenzel W. Modeling loop backbone flexibility in receptor-ligand docking simulations. J Comput Chem. 2012; 33(31):2504\u201315.","journal-title":"J Comput Chem"},{"key":"2222_CR35","volume-title":"32nd Brazilian Symposium on Databases (SBBD)","author":"R De Paris","year":"2017","unstructured":"De Paris R, Quevedo CV, Ruiz DA, Norberto de Souza O. An effective method to optimize docking-based virtual screening of fully-flexilbe receptor models. In: 32nd Brazilian Symposium on Databases (SBBD). Minas Gerais: Brazilian Computer Society: 2017. p. 316\u201325."},{"issue":"5204","key":"2222_CR36","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.1126\/science.7886450","volume":"267","author":"A Dessen","year":"1995","unstructured":"Dessen A, Quemard A, Blanchard JS, Jacobs Jr WR, Sacchettini JC. Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science. 1995; 267(5204):1638\u201341.","journal-title":"Science"},{"issue":"22","key":"2222_CR37","doi-asserted-by":"publisher","first-page":"15582","DOI":"10.1074\/jbc.274.22.15582","volume":"274","author":"DA Rozwarski","year":"1999","unstructured":"Rozwarski DA, Vilch\u00e8ze C, Sugantino M, Bittman R, Sacchettini JC. Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate. J Biol Chem. 1999; 274(22):15582\u20139.","journal-title":"J Biol Chem"},{"issue":"10","key":"2222_CR38","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1002\/emmm.201201689","volume":"4","author":"RC Hartkoorn","year":"2012","unstructured":"Hartkoorn RC, Sala C, Neres J, Pojer F, Magnet S, Mukherjee R, Uplekar S, Boy-R\u00f6ttger S, Altmann K-H, Cole ST. Towards a new tuberculosis drug: pyridomycin\u2013nature\u2019s isoniazid. EMBO Mol Med. 2012; 4(10):1032\u201342.","journal-title":"EMBO Mol Med"},{"key":"2222_CR39","volume-title":"AMBER 12","author":"D Case","year":"2016","unstructured":"Case D, Darden T, Cheatham III T, Simmerling C, Wang J, Duke R, Luo R, Walker R, Zhang W, Merz K, et al. AMBER 12. San Francisco: University of California; 2016."},{"issue":"3","key":"2222_CR40","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1002\/prot.21123","volume":"65","author":"V Hornak","year":"2006","unstructured":"Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins Struct Funct Bioinforma. 2006; 65(3):712\u201325.","journal-title":"Proteins Struct Funct Bioinforma"},{"key":"2222_CR41","unstructured":"Gargano F. Effect of temperature on the enzyme 2-trans-enoil-ACP(CoA) redutase (EC 1.3.1.9) of Mycobacterium tuberculosis in complex with the NADH: a study by molecular dynamic simulation. PhD thesis, Postgraduate Program in Cellular and Molecular Biology, PUCRS, Porto Alegre, RS, Brasil. 2009. (in Portuguese)."},{"key":"2222_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2015\/916240","volume":"2015","author":"R De Paris","year":"2015","unstructured":"De Paris R, Quevedo CV, Ruiz DD, Norberto de Souza O, Barros RC. Clustering molecular dynamics trajectories for optimizing docking experiments. Comput Intell Neurosci. 2015; 2015:1\u201310.","journal-title":"Comput Intell Neurosci"},{"issue":"1983","key":"2222_CR43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1098\/rsta.2012.0085","volume":"371","author":"H Hiden","year":"2013","unstructured":"Hiden H, Woodman S, Watson P, Cala J. Developing cloud applications using the e-science central platform. Philos Trans R Soc Lond A Math Phys Eng Sci. 2013; 371(1983):1\u201312.","journal-title":"Philos Trans R Soc Lond A Math Phys Eng Sci"},{"key":"2222_CR44","volume-title":"MongoDB: the Definitive Guide","author":"K Chodorow","year":"2013","unstructured":"Chodorow K. MongoDB: the Definitive Guide. Sebastopol: O\u2019Reilly Media; 2013."},{"key":"2222_CR45","unstructured":"Microsoft Azure: The cloud for modern business. https:\/\/azure.microsoft.com\/ . Accessed 20 Sep 2017."},{"key":"2222_CR46","unstructured":"Horizon: Horizon: The OpenStack Dashboard Project. 2016. http:\/\/docs.openstack.org\/developer\/horizon\/ . Accessed 10 June 2016."},{"issue":"7","key":"2222_CR47","doi-asserted-by":"publisher","first-page":"1860","DOI":"10.1016\/j.future.2013.01.011","volume":"29","author":"J Ca\u0142a","year":"2013","unstructured":"Ca\u0142a J, Hiden H, Woodman S, Watson P. Cloud computing for fast prediction of chemical activity. Futur Gener Comput Syst. 2013; 29(7):1860\u20139.","journal-title":"Futur Gener Comput Syst"},{"key":"2222_CR48","doi-asserted-by":"crossref","unstructured":"H\u00fcbler P, Ruiz D, Ferreira JE, Norberto de Souza O. P-SaMI: a data-flow pattern to perform massively-parallel molecular docking experiments using a fully-flexible receptor model. In: 30th Annual ACM Symposium on Applied Computing. Salamanca: Association for Computing Machinery: 2015. p. 54\u201357.","DOI":"10.1145\/2695664.2695962"},{"issue":"1","key":"2222_CR49","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1021\/cb0500042","volume":"1","author":"TJ Sullivan","year":"2006","unstructured":"Sullivan TJ, Truglio JJ, Boyne ME, Novichenok P, Zhang X, Stratton CF, Li H-J, Kaur T, Amin A, Johnson F, et al. High affinity InhA inhibitors with activity against drug-resistant strains of Mycobacterium tuberculosis. ACS Chem Biol. 2006; 1(1):43\u201353.","journal-title":"ACS Chem Biol"},{"issue":"1","key":"2222_CR50","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res. 2000; 28(1):235\u201342.","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"2222_CR51","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1021\/ci3001277","volume":"52","author":"JJ Irwin","year":"2012","unstructured":"Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012; 52(7):1757\u201368.","journal-title":"J Chem Inf Model"},{"issue":"W1","key":"2222_CR52","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1093\/nar\/gks378","volume":"40","author":"DR Koes","year":"2012","unstructured":"Koes DR, Camacho CJ. Zincpharmer: pharmacophore search of the zinc database. Nucleic Acids Res. 2012; 40(W1):409\u201314.","journal-title":"Nucleic Acids Res"},{"key":"2222_CR53","unstructured":"World Health Organization (WHO). Global tuberculosis report 2016. http:\/\/apps.who.int\/medicinedocs\/documents\/s23098en\/s23098en.pdf ."},{"key":"2222_CR54","unstructured":"Quevedo CV. Virtual Screening in Ligand Databases Considering Phisical-Chemical Properties of Fully-Flexible Receptor Model. PhD thesis, School of Technology, PUCRS, Porto Alegre, RS, Brasil. 2016. (in Portuguese)."},{"issue":"6","key":"2222_CR55","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1002\/jcc.20634","volume":"28","author":"R Huey","year":"2007","unstructured":"Huey R, Morris GM, Olson AJ, Goodsell DS. A semiempirical free energy force field with charge-based desolvation. J Comput Chem. 2007; 28(6):1145\u201352.","journal-title":"J Comput Chem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2222-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2222-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2222-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,19]],"date-time":"2019-10-19T17:07:46Z","timestamp":1571504866000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2222-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,22]]},"references-count":55,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2222"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2222-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,6,22]]},"assertion":[{"value":"8 November 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 May 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 June 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"This research does not involve human subjects, human material or human data.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"This manuscript does not contain details, images or videos relating to an individual person.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"235"}}