{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:28:34Z","timestamp":1740144514558,"version":"3.37.3"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T00:00:00Z","timestamp":1590364800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T00:00:00Z","timestamp":1590364800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM123131"],"award-info":[{"award-number":["R01GM123131"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Algorithms Mol Biol"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Geometric comparisons of binding sites and their electrostatic properties can identify subtle variations that select different binding partners and subtle similarities that accommodate similar partners. Because subtle features are central for explaining how proteins achieve specificity, algorithmic efficiency and geometric precision are central to algorithmic design. To address these concerns, this paper presents pClay, the first algorithm to perform parallel and arbitrarily precise comparisons of molecular surfaces and electrostatic isopotentials as geometric solids. pClay was presented at the 2019 Workshop on Algorithms in Bioinformatics (WABI 2019) and is described in expanded detail here, especially with regard to the comparison of electrostatic isopotentials. Earlier methods have generally used parallelism to enhance computational throughput, pClay is the first algorithm to use parallelism to make arbitrarily high precision comparisons practical. It is also the first method to demonstrate that high precision comparisons of geometric solids can yield more precise structural inferences than algorithms that use existing standards of precision. One advantage of added precision is that statistical models can be trained with more accurate data. Using structural data from an existing method, a model of steric variations between binding cavities can overlook 53% of authentic steric influences on specificity, whereas a model trained with data from pClay overlooks none. Our results also demonstrate the parallel performance of pClay on both workstation CPUs and a 61-core Xeon Phi. While slower on one core, additional processor cores rapidly outpaced single core performance and existing methods. Based on these results, it is clear that pClay has applications in the automatic explanation of binding mechanisms and in the rational design of protein binding preferences.<\/jats:p>","DOI":"10.1186\/s13015-020-00168-z","type":"journal-article","created":{"date-parts":[[2020,5,25]],"date-time":"2020-05-25T04:02:26Z","timestamp":1590379346000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials"],"prefix":"10.1186","volume":"15","author":[{"given":"Georgi D.","family":"Georgiev","sequence":"first","affiliation":[]},{"given":"Kevin F.","family":"Dodd","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9025-0107","authenticated-orcid":false,"given":"Brian Y.","family":"Chen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,5,25]]},"reference":[{"issue":"5","key":"168_CR1","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\u201316.","journal-title":"J Mol Biol"},{"issue":"2","key":"168_CR2","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\u201326.","journal-title":"J Mol Biol"},{"issue":"1","key":"168_CR3","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1186\/1471-2105-6-194","volume":"6","author":"F Ferre","year":"2005","unstructured":"Ferre F, Ausiello G, Zanzoni A, Helmer-Citterich M. Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinform. 2005;6(1):194.","journal-title":"BMC Bioinform"},{"issue":"6","key":"168_CR4","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1089\/cmb.2007.R017","volume":"14","author":"BY Chen","year":"2007","unstructured":"Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE. The mash pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs. J Comput Biol. 2007;14(6):791\u2013816.","journal-title":"J Comput Biol"},{"issue":"1","key":"168_CR5","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1073\/pnas.0707684105","volume":"105","author":"M Brylinski","year":"2008","unstructured":"Brylinski M, Skolnick J. A threading-based method (findsite) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci. 2008;105(1):129\u201334.","journal-title":"Proc Natl Acad Sci"},{"doi-asserted-by":"crossref","unstructured":"Meng EC, Polacco BJ, Babbitt PC. 3D motifs. In: From protein structure to function with bioinformatics. Berlin: Springer; 2009. p. 187\u2013216.","key":"168_CR6","DOI":"10.1007\/978-1-4020-9058-5_8"},{"issue":"1","key":"168_CR7","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1186\/1471-2105-11-555","volume":"11","author":"M Moll","year":"2010","unstructured":"Moll M, Bryant DH, Kavraki LE. The labelhash algorithm for substructure matching. BMC bioinformatics. 2010;11(1):555.","journal-title":"BMC bioinformatics"},{"issue":"3","key":"168_CR8","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1109\/TCBB.2009.28","volume":"8","author":"J Venkateswaran","year":"2011","unstructured":"Venkateswaran J, Song B, Kahveci T, Jermaine C. Trial: a tool for finding distant structural similarities. IEEE\/ACM Trans Comput Biol Bioinform. 2011;8(3):819\u201331.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"7","key":"168_CR9","doi-asserted-by":"publisher","first-page":"40540","DOI":"10.1371\/journal.pone.0040540","volume":"7","author":"L Ellingson","year":"2012","unstructured":"Ellingson L, Zhang J. Protein surface matching by combining local and global geometric information. PloS ONE. 2012;7(7):40540.","journal-title":"PloS ONE"},{"issue":"2","key":"168_CR10","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1089\/cmb.2012.0246","volume":"20","author":"L He","year":"2013","unstructured":"He L, Vandin F, Pandurangan G, Bailey-Kellogg C. Ballast: a ball-based algorithm for structural motifs. J Comput Biol. 2013;20(2):137\u201351.","journal-title":"J Comput Biol"},{"issue":"7","key":"168_CR11","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1089\/cmb.2014.0263","volume":"22","author":"F Kaiser","year":"2015","unstructured":"Kaiser F, Eisold A, Labudde D. A novel algorithm for enhanced structural motif matching in proteins. J Comput Biol. 2015;22(7):698\u2013713.","journal-title":"J Comput Biol"},{"issue":"suppl\u20132","key":"168_CR12","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1093\/nar\/gkm351","volume":"35","author":"K Kinoshita","year":"2007","unstructured":"Kinoshita K, Murakami Y, Nakamura H. ef-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. 2007;35(suppl\u20132):398\u2013402.","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"168_CR13","doi-asserted-by":"publisher","first-page":"1003792","DOI":"10.1371\/journal.pcbi.1003792","volume":"10","author":"BY Chen","year":"2014","unstructured":"Chen BY. Vasp-e: specificity annotation with a volumetric analysis of electrostatic isopotentials. PLoS Comput Biol. 2014;10(8):1003792.","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"168_CR14","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1089\/cmb.2016.0162","volume":"24","author":"BE Nolan","year":"2017","unstructured":"Nolan BE, Levenson E, Chen BY. Influential mutations in the smad4 trimer complex can be detected from disruptions of electrostatic complementarity. J Comput Biol. 2017;24(1):68\u201378.","journal-title":"J Comput Biol"},{"key":"168_CR15","doi-asserted-by":"publisher","first-page":"42912","DOI":"10.1038\/srep42912","volume":"7","author":"Y Zhou","year":"2017","unstructured":"Zhou Y, Li X-P, Chen BY, Tumer NE. Ricin uses arginine 235 as an anchor residue to bind to p-proteins of the ribosomal stalk. Sci Rep. 2017;7:42912.","journal-title":"Sci Rep"},{"doi-asserted-by":"crossref","unstructured":"Chen BY, Bandyopadhyay S. Vasp-s: a volumetric analysis and statistical model for predicting steric influences on protein-ligand binding specificity. In: 2011 IEEE international conference on bioinformatics and biomedicine (BIBM). New York: IEEE; 2011. p. 22\u20139.","key":"168_CR16","DOI":"10.1109\/BIBM.2011.33"},{"key":"168_CR17","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1477-5956-10-S1-S6","volume":"10","author":"BY Chen","year":"2012","unstructured":"Chen BY, Bandyopadhyay S. Modeling regionalized volumetric differences in protein-ligand binding cavities. Proteome Sci. 2012;10:6 BioMed Central.","journal-title":"Proteome Sci"},{"doi-asserted-by":"crossref","unstructured":"Chen BY, Bandyopadhyay S. A statistical model of overlapping volume in ligand binding cavities. In: 2011 IEEE international conference on bioinformatics and biomedicine workshops (BIBMW). New York: IEEE; 2011. p. 424\u201331.","key":"168_CR18","DOI":"10.1109\/BIBMW.2011.6112409"},{"issue":"03","key":"168_CR19","doi-asserted-by":"publisher","first-page":"1242004","DOI":"10.1142\/S0219720012420048","volume":"10","author":"BY Chen","year":"2012","unstructured":"Chen BY, Bandyopadhyay S. A regionalizable statistical model of intersecting regions in protein-ligand binding cavities. J Bioinform Comput Biol. 2012;10(03):1242004.","journal-title":"J Bioinform Comput Biol"},{"doi-asserted-by":"crossref","unstructured":"Okun RY, Chen BY. A statistical model of electrostatic isopotential variation in serine protease binding cavities. In: 2015 IEEE international conference on bioinformatics and biomedicine (BIBM). New York: IEEE; 2015. p. 1246\u201352.","key":"168_CR20","DOI":"10.1109\/BIBM.2015.7359859"},{"issue":"8","key":"168_CR21","doi-asserted-by":"publisher","first-page":"1000881","DOI":"10.1371\/journal.pcbi.1000881","volume":"6","author":"BY Chen","year":"2010","unstructured":"Chen BY, Honig B. Vasp: a volumetric analysis of surface properties yields insights into protein-ligand binding specificity. PLoS Comput Biol. 2010;6(8):1000881.","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"168_CR22","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1016\/S0968-0896(98)00099-6","volume":"6","author":"Y Liu","year":"1998","unstructured":"Liu Y, Shah K, Yang F, Witucki L, Shokat K. A molecular gate which controls unnatural atp analogue recognition by the tyrosine kinase v-src. Bioorg Med Chem. 1998;6(8):1219\u201326.","journal-title":"Bioorg Med Chem"},{"issue":"3","key":"168_CR23","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","volume":"55","author":"B Lee","year":"1971","unstructured":"Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971;55(3):379\u201384.","journal-title":"J Mol Biol"},{"issue":"5","key":"168_CR24","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1107\/S0021889883010985","volume":"16","author":"ML Connolly","year":"1983","unstructured":"Connolly ML. Analytical molecular surface calculation. J Appl Crystallogr. 1983;16(5):548\u201358.","journal-title":"J Appl Crystallogr"},{"key":"168_CR25","first-page":"492","volume-title":"Methods in Enzymology","author":"Donald Petrey","year":"2003","unstructured":"Petrey D, Honig B. Grasp2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. In: Methods in enzymology vol. 374. Amsterdam: Elsevier; 2003. p. 492\u2013509."},{"issue":"4","key":"168_CR26","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1145\/37402.37422","volume":"21","author":"William E. Lorensen","year":"1987","unstructured":"Lorensen WE, Cline HE. Marching cubes: A high resolution 3D surface construction algorithm. In: ACM Siggraph Computer Graphics, ACM. 1987;21:163\u20139.","journal-title":"ACM SIGGRAPH Computer Graphics"},{"issue":"3","key":"168_CR27","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1145\/566654.566586","volume":"21","author":"Tao Ju","year":"2002","unstructured":"Ju T, Losasso F, Schaefer S, Warren J. Dual contouring of hermite data. In: ACM Transactions on Graphics (TOG), ACM. 2002;21:339\u201346.","journal-title":"ACM Transactions on Graphics (TOG)"},{"issue":"2","key":"168_CR28","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/0022-2836(73)90011-9","volume":"79","author":"A Shrake","year":"1973","unstructured":"Shrake A, Rupley J. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol. 1973;79(2):351\u201371.","journal-title":"J Mol Biol"},{"issue":"3","key":"168_CR29","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1002\/(SICI)1097-0282(199603)38:3<305::AID-BIP4>3.0.CO;2-Y","volume":"38","author":"MF Sanner","year":"1996","unstructured":"Sanner MF, Olson AJ, Spehner J-C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996;38(3):305\u201320.","journal-title":"Biopolymers"},{"issue":"11","key":"168_CR30","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.1002\/(SICI)1096-987X(199808)19:11<1268::AID-JCC6>3.0.CO;2-I","volume":"19","author":"SL Chan","year":"1998","unstructured":"Chan SL, Purisima EO. Molecular surface generation using marching tetrahedra. J Comput Chem. 1998;19(11):1268\u201377.","journal-title":"J Comput Chem"},{"issue":"1","key":"168_CR31","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1002\/jcc.1161","volume":"23","author":"W Rocchia","year":"2002","unstructured":"Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J Comput Chem. 2002;23(1):128\u201337.","journal-title":"J Comput Chem"},{"key":"168_CR32","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.jmgm.2012.07.004","volume":"38","author":"T Lu","year":"2012","unstructured":"Lu T, Chen F. Quantitative analysis of molecular surface based on improved marching tetrahedra algorithm. J Mol Graph Model. 2012;38:314\u201323.","journal-title":"J Mol Graph Model"},{"unstructured":"DeLano WL. The pymol molecular graphics system. 2002. http:\/\/pymol.org.","key":"168_CR33"},{"issue":"13","key":"168_CR34","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. Ucsf chimera\u2014a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605\u201312.","journal-title":"J Comput Chem"},{"issue":"1\u20133","key":"168_CR35","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/S0166-218X(98)00067-5","volume":"88","author":"H Edelsbrunner","year":"1998","unstructured":"Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. Discrete Appl Math. 1998;88(1\u20133):83\u2013102.","journal-title":"Discrete Appl Math"},{"issue":"1","key":"168_CR36","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/S0166-218X(02)00283-4","volume":"127","author":"CL Bajaj","year":"2003","unstructured":"Bajaj CL, Pascucci V, Shamir A, Holt RJ, Netravali AN. Dynamic maintenance and visualization of molecular surfaces. Discrete Appl Math. 2003;127(1):23\u201351.","journal-title":"Discrete Appl Math"},{"issue":"3","key":"168_CR37","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.bpj.2017.11.325","volume":"114","author":"W Tian","year":"2018","unstructured":"Tian W, Chen C, Liang J. Castp 3.0: computed atlas of surface topography of proteins and beyond. Biophys J. 2018;114(3):50.","journal-title":"Biophys J"},{"issue":"4","key":"168_CR38","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1109\/38.7748","volume":"8","author":"NL Max","year":"1988","unstructured":"Max NL, Getzoff ED. Spherical harmonic molecular surfaces. IEEE Comput Graph Appl. 1988;8(4):42\u201350.","journal-title":"IEEE Comput Graph Appl"},{"issue":"10","key":"168_CR39","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1093\/bioinformatics\/bti337","volume":"21","author":"RJ Morris","year":"2005","unstructured":"Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics. 2005;21(10):2347\u201355.","journal-title":"Bioinformatics"},{"issue":"27","key":"168_CR40","doi-asserted-by":"publisher","first-page":"2199","DOI":"10.1002\/jcc.23048","volume":"33","author":"J Konc","year":"2012","unstructured":"Konc J, Depolli M, Trobec R, Rozman K, Jane\u017ei\u010d D. Parallel-probis: fast parallel algorithm for local structural comparison of protein structures and binding sites. J Comput Chem. 2012;33(27):2199\u2013203.","journal-title":"J Comput Chem"},{"doi-asserted-by":"crossref","unstructured":"Hung C-L, Lin Y-L. Implementation of a parallel protein structure alignment service on cloud. Int Jo Genomics. 2013;2013.","key":"168_CR41","DOI":"10.1155\/2013\/439681"},{"issue":"3","key":"168_CR42","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1109\/38.28107","volume":"9","author":"J Goldfeather","year":"1989","unstructured":"Goldfeather J, Monar S, Turk G, Fuchs H. Near real-time CSG rendering using tree normalization and geometric pruning. IEEE Comput Graph Appl. 1989;9(3):20\u20138.","journal-title":"IEEE Comput Graph Appl"},{"doi-asserted-by":"crossref","unstructured":"Banerjee RP, Goel V, Mukherjee A. Efficient parallel evaluation of CSG tree using fixed number of processors. In: Proceedings on the second ACM symposium on solid modeling and applications. New York: ACM; 1993. p. 137\u201346.","key":"168_CR43","DOI":"10.1145\/164360.164409"},{"doi-asserted-by":"crossref","unstructured":"Martin WA, Fateman RJ. The macsyma system. In: Proceedings of the second ACM symposium on symbolic and algebraic manipulation. New York: ACM; 1971. p. 59\u201375.","key":"168_CR44","DOI":"10.1145\/800204.806267"},{"issue":"1","key":"168_CR45","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1137\/0216006","volume":"16","author":"F Aurenhammer","year":"1987","unstructured":"Aurenhammer F. Power diagrams: properties, algorithms and applications. SIAM J Comput. 1987;16(1):78\u201396.","journal-title":"SIAM J Comput"},{"doi-asserted-by":"crossref","unstructured":"Bernal J. Regtet: A program for computing regular tetrahedralizations. In: International conference on computational science. Berlin: Springer; 2001. p. 629\u201332.","key":"168_CR46","DOI":"10.1007\/3-540-45545-0_72"},{"issue":"1","key":"168_CR47","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/2046-1682-5-9","volume":"5","author":"L Li","year":"2012","unstructured":"Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z, Wang L, Smith N, Petukh M, Alexov E. Delphi: a comprehensive suite for delphi software and associated resources. BMC Biophys. 2012;5(1):9.","journal-title":"BMC Biophys"},{"issue":"suppl\u20132","key":"168_CR48","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1093\/nar\/gkr468","volume":"39","author":"M Fischer","year":"2011","unstructured":"Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D. Markus: a server to navigate sequence-structure-function space. Nucleic Acids Res. 2011;39(suppl\u20132):357\u201361.","journal-title":"Nucleic Acids Res"},{"doi-asserted-by":"crossref","unstructured":"Schaer J, Stone M. Face traverses and a volume algorithm for polyhedra. In: New results and new trends in computer science. Berlin: Springer; 1991. p. 290\u201397.","key":"168_CR49","DOI":"10.1007\/BFb0038197"},{"doi-asserted-by":"crossref","unstructured":"Godshall BG, Chen BY. Improving accuracy in binding site comparison with homology modeling. In: IEEE international conference on bioinformatics and biomedicine workshops (BIBMW), 2012. New York: IEEE;2012. p. 662\u20139.","key":"168_CR50","DOI":"10.1109\/BIBMW.2012.6470291"},{"issue":"5","key":"168_CR51","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1109\/TCBB.2013.124","volume":"10","author":"S Blumenthal","year":"2013","unstructured":"Blumenthal S, Tang Y, Yang W, Chen BY. Isolating influential regions of electrostatic focusing in protein and DNA structure. IEEE\/ACM Trans Comput Biol Bioinform. 2013;10(5):1188\u201398.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"4","key":"168_CR52","doi-asserted-by":"publisher","first-page":"892","DOI":"10.1002\/prot.20897","volume":"63","author":"M Nayal","year":"2006","unstructured":"Nayal M, Honig B. On the nature of cavities on protein surfaces: application to the identification of drug-binding sites. Proteins: Struct Funct Bioinform. 2006;63(4):892\u2013906.","journal-title":"Proteins: Struct Funct Bioinform"},{"issue":"3","key":"168_CR53","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1006\/jmbi.2000.3973","volume":"301","author":"A-S Yang","year":"2000","unstructured":"Yang A-S, Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance1. J Mol Biol. 2000;301(3):665\u201378.","journal-title":"J Mol Biol"},{"issue":"D1","key":"168_CR54","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1093\/nar\/gkt1208","volume":"42","author":"T Madej","year":"2013","unstructured":"Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. Mmdb and vast+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2013;42(D1):297\u2013303.","journal-title":"Nucleic Acids Res"}],"container-title":["Algorithms for Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13015-020-00168-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13015-020-00168-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13015-020-00168-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T23:09:01Z","timestamp":1621897741000},"score":1,"resource":{"primary":{"URL":"https:\/\/almob.biomedcentral.com\/articles\/10.1186\/s13015-020-00168-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,25]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["168"],"URL":"https:\/\/doi.org\/10.1186\/s13015-020-00168-z","relation":{},"ISSN":["1748-7188"],"issn-type":[{"type":"electronic","value":"1748-7188"}],"subject":[],"published":{"date-parts":[[2020,5,25]]},"assertion":[{"value":"27 October 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 April 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 May 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","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"}}],"article-number":"11"}}