{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:29:36Z","timestamp":1725992976781},"reference-count":131,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20661-4","type":"book-chapter","created":{"date-parts":[[2018,5,18]],"date-time":"2018-05-18T21:56:15Z","timestamp":1526680575000},"page":"666-677","source":"Crossref","is-referenced-by-count":1,"title":["Protein-Carbohydrate Interactions"],"prefix":"10.1016","author":[{"given":"Adeel","family":"Malik","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad H.","family":"Baig","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balachandran","family":"Manavalan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib1","doi-asserted-by":"crossref","first-page":"e24039","DOI":"10.1371\/journal.pone.0024039","article-title":"Identification of mannose interacting residues using local composition","volume":"6","author":"Agarwal","year":"2011","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.sbi.2016.11.011","article-title":"Carbohydrate structure: The rocky road to automation","volume":"44","author":"Agirre","year":"2017","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib3","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.1021\/ci900388a","article-title":"Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures","volume":"49","author":"Agostino","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib4","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2105-6-33","article-title":"PSSM-based prediction of DNA binding sites in proteins","volume":"6","author":"Ahmad","year":"2005","journal-title":"BMC Bioinform."},{"year":"2014","series-title":"Introduction to Machine Learning","author":"Alpaydin","key":"10.1016\/B978-0-12-809633-8.20661-4_bib5"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib6","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: A new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib7","doi-asserted-by":"crossref","first-page":"11","DOI":"10.2174\/1389203033380322","article-title":"Mapping protein: Carbohydrate interactions","volume":"4","author":"Audette","year":"2003","journal-title":"Curr. Protein Pept. Sci."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib8","doi-asserted-by":"crossref","first-page":"E3111","DOI":"10.1073\/pnas.1519881113","article-title":"Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation","volume":"113","author":"Bakkers","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib9","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.compbiolchem.2016.10.009","article-title":"Development of a sugar-binding residue prediction system from protein sequences using support vector machine","volume":"66","author":"Banno","year":"2017","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib10","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/978-1-62703-748-8_7","article-title":"Introduction to machine learning","volume":"1107","author":"Bastanlar","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3109\/10242420903408252","article-title":"Substrate conformational changes in glycoside hydrolase catalysis. A first-principles molecular dynamics study","volume":"28","author":"Biarn\u00ebs","year":"2010","journal-title":"Biocatal. Biotransform."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib12","doi-asserted-by":"crossref","first-page":"3004","DOI":"10.1021\/ja983319g","article-title":"Docking of glycosaminoglycans to heparin-binding proteins: Validation for aFGF, bFGF, and antithrombin and application to IL-8","volume":"121","author":"Bitomsky","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib13","doi-asserted-by":"crossref","unstructured":"Brzozowska, E., Pyra, A., Mi\u015bk\u00f5w, M., G\u00f5rska, S., Gamian, A. 2015. C-terminal sequence determinants of T4 bacteriophage tail fiber adhesin for specific lipopolysaccharide recognition.","DOI":"10.15226\/sojmid\/3\/1\/00130"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib14","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkq361","article-title":"NAPS: A residue-level nucleic acid-binding prediction server","volume":"38","author":"Carson","year":"2010","journal-title":"Nucleic Acids Res."},{"issue":"Suppl. 15","key":"10.1016\/B978-0-12-809633-8.20661-4_bib15","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-15-S15-S4","article-title":"LigandRFs: Random forest ensemble to identify ligand-binding residues from sequence information alone","volume":"15","author":"Chen","year":"2014","journal-title":"BMC Bioinform."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib16","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/nchembio.155","article-title":"Molecular docking and ligand specificity in fragment-based inhibitor discovery","volume":"5","author":"Chen","year":"2009","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib17","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1021\/ci050026f","article-title":"Improved FlexX docking using FlexS-determined base fragment placement","volume":"45","author":"Cross","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib18","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1021\/cr000401x","article-title":"Thermodynamic studies of lectin-carbohydrate interactions by isothermal titration calorimetry","volume":"102","author":"Dam","year":"2002","journal-title":"Chem. Rev."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib19","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1002\/prot.22356","article-title":"Characterization of a diagnostic Fab fragment binding trimeric Lewis X","volume":"76","author":"De Geus","year":"2009","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib20","doi-asserted-by":"crossref","unstructured":"De Schutter, K., Van Damme, E.J., 2015. Protein-carbohydrate interactions, and beyond. Multidisciplinary Digital Publishing Institute.","DOI":"10.3390\/molecules200815202"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib21","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1007\/s00894-001-0055-8","article-title":"AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages","volume":"7","author":"Dejoux","year":"2001","journal-title":"J. Mol. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib22","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/glycob\/cwn026","article-title":"Structural glycobiology: A game of snakes and ladders","volume":"18","author":"DeMarco","year":"2008","journal-title":"Glycobiology"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib230","doi-asserted-by":"crossref","first-page":"e0183060","DOI":"10.1371\/journal.pone.0183060","article-title":"Rational design of drug-like compounds targeting Mycobacterium marinum MelF protein","volume":"12","author":"Dharra","year":"2017","journal-title":"PLoS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib23","doi-asserted-by":"crossref","first-page":"197","DOI":"10.2174\/157340910791760091","article-title":"Computational prediction of DNA-protein interactions: A review","volume":"6","author":"Ding","year":"2010","journal-title":"Curr. Comput. Aided Drug Des."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib24","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/S0300-9084(03)00060-9","article-title":"Carbohydrate-lectin interactions assessed by surface plasmon resonance","volume":"85","author":"Duverger","year":"2003","journal-title":"Biochimie"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib25","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics (Oxford)"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib26","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1016\/j.drudis.2010.06.001","article-title":"Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects","volume":"15","author":"Fadda","year":"2010","journal-title":"Drug Discov. Today"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib27","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1046\/j.1432-1033.2002.02767.x","article-title":"Prediction of protein\u2013protein interaction sites in heterocomplexes with neural networks","volume":"269","author":"Fariselli","year":"2002","journal-title":"Eur. J. Biochem."},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20661-4_bib28","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1471-2091-12-20","article-title":"Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates","volume":"13","author":"Firoz","year":"2011","journal-title":"BMC Biochem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib29","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy","volume":"47","author":"Friesner","year":"2004","journal-title":"J. Med. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib30","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1038\/nbt735","article-title":"Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate-protein interactions","volume":"20","author":"Fukui","year":"2002","journal-title":"Nature Biotechnol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib31","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1006\/jmbi.2000.4092","article-title":"A fast method to predict protein interaction sites from sequences","volume":"302","author":"Gallet","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib32","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/glycob\/cws147","article-title":"Solvent structure improves docking prediction in lectin-carbohydrate complexes","volume":"23","author":"Gauto","year":"2013","journal-title":"Glycobiology"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib33","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/S0263-7855(97)00010-6","article-title":"Knowledge-based modeling of a legume lectin and docking of the carbohydrate ligand: The Ulex europaeus lectin I and its interaction with fucose","volume":"14","author":"Gohier","year":"1996","journal-title":"J. Mol. Graph."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib34","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/s13068-016-0605-z","article-title":"Structural and functional characterization of a highly stable endo-beta-1,4-xylanase from Fusarium oxysporum and its development as an efficient immobilized biocatalyst","volume":"9","author":"Gomez","year":"2016","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib35","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.sbi.2014.07.001","article-title":"Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins","volume":"28","author":"Grant","year":"2014","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib36","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/0076-6879(90)83011-W","article-title":"Profile analysis","volume":"183","author":"Gribskov","year":"1990","journal-title":"Methods Enzymol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib37","doi-asserted-by":"crossref","first-page":"799","DOI":"10.2174\/09298665113209990055","article-title":"Identification and analysis of binding site residues in protein-carbohydrate complexes using energy based approach","volume":"21","author":"Gromiha","year":"2014","journal-title":"Protein Pept. Lett."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib38","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.03249-16","article-title":"Transcriptomic analyses elucidate adaptive differences of closely related strains of pseudomonas aeruginosa in fuel","volume":"83","author":"Gunasekera","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib39","doi-asserted-by":"crossref","first-page":"2543","DOI":"10.1002\/jcc.21004","article-title":"Additive empirical force field for hexopyranose monosaccharides","volume":"29","author":"Guvench","year":"2008","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib40","doi-asserted-by":"crossref","first-page":"2353","DOI":"10.1021\/ct900242e","article-title":"CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses","volume":"5","author":"Guvench","year":"2009","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib41","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/S0959-440X(02)00308-1","article-title":"Molecular dynamics simulations","volume":"12","author":"Hansson","year":"2002","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib42","doi-asserted-by":"crossref","first-page":"12466","DOI":"10.1021\/jp905496e","article-title":"CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose","volume":"113","author":"Hatcher","year":"2009","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib43","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1002\/jcc.20873","article-title":"A Gibbs free energy correlation for automated docking of carbohydrates","volume":"29","author":"Hill","year":"2008","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib44","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/bioinformatics\/btl672","article-title":"DP-Bind: A web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins","volume":"23","author":"Hwang","year":"2007","journal-title":"Bioinformatics"},{"issue":"33\u201338","key":"10.1016\/B978-0-12-809633-8.20661-4_bib450","first-page":"27","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib45","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/S0959-440X(97)80069-3","article-title":"Oligosaccharide structures: Theory versus experiment","volume":"7","author":"Imberty","year":"1997","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib46","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/S0959-440X(99)00004-4","article-title":"Free and protein-bound carbohydrate structures","volume":"9","author":"Jim\u00ebnez-Barbero","year":"1999","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib47","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/0165-6147(91)90568-D","article-title":"Glycobiology: A growing field for drug design","volume":"12","author":"Karlsson","year":"1991","journal-title":"Trends Pharmacol. Sci."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib48","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/widm.48","article-title":"Computational tools for protein\u2013DNA interactions","volume":"2","author":"Kaufman","year":"2012","journal-title":"WIREs Data Mining Knowl. Discov."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib49","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1021\/ci800103u","article-title":"BALLDock\/SLICK: A new method for protein-carbohydrate docking","volume":"48","author":"Kerzmann","year":"2008","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib50","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1021\/ci050422y","article-title":"SLICK \u2013 Scoring and energy functions for protein-carbohydrate interactions","volume":"46","author":"Kerzmann","year":"2006","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib51","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.6026\/97320630081202","article-title":"Prediction of protein-mannose binding sites using random forest","volume":"8","author":"Khare","year":"2012","journal-title":"Bioinformation"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib52","doi-asserted-by":"crossref","first-page":"10541","DOI":"10.1073\/pnas.191362798","article-title":"Solvent interactions determine carbohydrate conformation","volume":"98","author":"Kirschner","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib53","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1002\/jcc.20820","article-title":"GLYCAM06: A generalizable biomolecular force field. Carbohydrates","volume":"29","author":"Kirschner","year":"2008","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib54","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/0022-2836(90)90154-E","article-title":"Improvements in protein secondary structure prediction by an enhanced neural network","volume":"214","author":"Kneller","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib55","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1002\/jcc.10139","article-title":"An improved OPLS-AA force field for carbohydrates","volume":"23","author":"Kony","year":"2002","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib56","doi-asserted-by":"crossref","first-page":"4768","DOI":"10.1093\/nar\/22.22.4768","article-title":"A hidden Markov model that finds genes in E. coli DNA","volume":"22","author":"Krogh","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib57","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.jmgm.2009.08.009","article-title":"InCa-SiteFinder: A method for structure-based prediction of inositol and carbohydrate binding sites on proteins","volume":"28","author":"Kulharia","year":"2009","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib58","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1002\/prot.20977","article-title":"Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins","volume":"64","author":"Kuznetsov","year":"2006","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib59","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1002\/jcc.24679","article-title":"Residue-centric modeling and design of saccharide and glycoconjugate structures","volume":"38","author":"Labonte","year":"2017","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib60","doi-asserted-by":"crossref","first-page":"1748","DOI":"10.1002\/jcc.10288","article-title":"Specific empirical free energy function for automated docking of carbohydrates to proteins","volume":"24","author":"Laederach","year":"2003","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib61","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","article-title":"Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites","volume":"21","author":"Laurie","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib62","doi-asserted-by":"crossref","first-page":"14352","DOI":"10.1038\/srep14352","article-title":"Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation","volume":"5","author":"Lawrence","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib63","doi-asserted-by":"crossref","first-page":"e43927","DOI":"10.1371\/journal.pone.0043927","article-title":"Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS","volume":"7","author":"Li","year":"2012","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib64","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1002\/jcc.20275","article-title":"A new GROMOS force field for hexopyranose-based carbohydrates","volume":"26","author":"Lins","year":"2005","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib65","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/0076-6879(72)28046-6","article-title":"Soy bean (Glycine max) agglutinin","volume":"28","author":"Lis","year":"1972","journal-title":"Methods Enzymol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib66","doi-asserted-by":"crossref","first-page":"3522","DOI":"10.1093\/nar\/gkh684","article-title":"Sequence-based prediction of protein domains","volume":"32","author":"Liu","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib67","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1093\/bioinformatics\/9.6.745","article-title":"Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation","volume":"9","author":"Livingstone","year":"1993","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib68","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib69","doi-asserted-by":"crossref","first-page":"1400","DOI":"10.1002\/jcc.20065","article-title":"Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations","volume":"25","author":"MacKerell","year":"2004","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib70","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1472-6807-7-1","article-title":"Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network","volume":"7","author":"Malik","year":"2007","journal-title":"BMC Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib71","first-page":"436036","article-title":"PROCARB: A database of known and modelled carbohydrate-binding protein structures with sequence-based prediction tools","author":"Malik","year":"2010","journal-title":"Adv. Bioinform"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib72","doi-asserted-by":"crossref","first-page":"e95480","DOI":"10.1371\/journal.pone.0095480","article-title":"Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data","volume":"9","author":"Malik","year":"2014","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib73","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1007\/978-1-4939-2343-4_25","article-title":"Molecular dynamics simulations of glycoproteins using CHARMM","volume":"1273","author":"Mallajosyula","year":"2015","journal-title":"Methods Mol. Biol."},{"issue":"44","key":"10.1016\/B978-0-12-809633-8.20661-4_bib74","doi-asserted-by":"crossref","first-page":"77121","DOI":"10.18632\/oncotarget.20365","article-title":"MLACP: Machine-learning-based prediction of anticancer peptides","volume":"8","author":"Manavalan","year":"2017","journal-title":"Oncotarget"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib75","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/btx222","article-title":"SVMQA: Support-vector-machine-based protein single-model quality assessment","volume":"33","author":"Manavalan","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib76","doi-asserted-by":"crossref","first-page":"e106542","DOI":"10.1371\/journal.pone.0106542","article-title":"Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms","volume":"9","author":"Manavalan","year":"2014","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib77","article-title":"DHSpred: Support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest","author":"Manavalan","year":"2017","journal-title":"Oncotarget"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib78","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0003-2697(83)90613-9","article-title":"Enzyme-linked lectin assay (ELLA): Use of alkaline phosphatase-conjugated Griffonia simplicifolia B4 isolectin for the detection of \u03b1-D-galactopyranosyl end groups","volume":"130","author":"McCoy","year":"1983","journal-title":"Anal. Biochem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib79","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1021\/ci200529n","article-title":"In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: Performance of docking software to predict saccharide binding","volume":"52","author":"Mishra","year":"2012","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib80","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1093\/glycob\/cwt093","article-title":"Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation","volume":"24","author":"Mishra","year":"2014","journal-title":"Glycobiology"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib81","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.jmgm.2017.02.007","article-title":"Insights into protein-carbohydrate recognition: A novel binding mechanism for CBM family 43","volume":"73","author":"Mompean","year":"2017","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib82","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0814s24","article-title":"Using AutoDock for ligand-receptor docking","author":"Morris","year":"2008","journal-title":"Curr. Protoc. Bioinform"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib83","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1002\/prot.20632","article-title":"Force calculations in automated docking: Enzyme-substrate interactions in Fusarium oxysporum Cel7B","volume":"61","author":"Mulakala","year":"2005","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib84","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/prot.22424","article-title":"Prediction of protein\u2010glucose binding sites using support vector machines","volume":"77","author":"Nassif","year":"2009","journal-title":"Proteins: Struct. Funct. Bioinform."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib85","doi-asserted-by":"crossref","first-page":"5248","DOI":"10.1021\/ja511237n","article-title":"Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins","volume":"137","author":"Ng","year":"2015","journal-title":"J. Am. Chem. Soc."},{"year":"1996","series-title":"Introduction to Machine Learning. An Early Draft of a Proposed Textbook","author":"Nilsson","key":"10.1016\/B978-0-12-809633-8.20661-4_bib86"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib87","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1002\/jcc.23517","article-title":"Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff","volume":"35","author":"Nivedha","year":"2014","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib88","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1021\/acs.jctc.5b00834","article-title":"Vina-Carb: Improving glycosidic angles during carbohydrate docking","volume":"12","author":"Nivedha","year":"2016","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib89","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/S0928-8244(03)00228-1","article-title":"Anti-adhesion therapy of bacterial diseases: Prospects and problems","volume":"38","author":"Ofek","year":"2003","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib90","doi-asserted-by":"crossref","first-page":"i347","DOI":"10.1093\/bioinformatics\/btm174","article-title":"Prediction of DNA-binding residues from sequence","volume":"23","author":"Ofran","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib91","doi-asserted-by":"crossref","first-page":"e119","DOI":"10.1371\/journal.pcbi.0030119","article-title":"Protein-protein interaction hotspots carved into sequences","volume":"3","author":"Ofran","year":"2007","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib92","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1080\/07391102.2015.1106978","article-title":"MOWGLI: Prediction of protein-Mannose interacting residues with ensemble classifiers using evolutionary information","volume":"34","author":"Pai","year":"2016","journal-title":"J. Biomol. Struct. Dyn."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib93","doi-asserted-by":"crossref","first-page":"2747","DOI":"10.1038\/nprot.2007.373","article-title":"Fabrication of carbohydrate chips and their use to probe protein-carbohydrate interactions","volume":"2","author":"Park","year":"2007","journal-title":"Nat. Protoc."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib94","doi-asserted-by":"crossref","first-page":"e1004037","DOI":"10.1371\/journal.ppat.1004037","article-title":"A role for LHC1 in higher order structure and complement binding of the Cryptococcus neoformans capsule","volume":"10","author":"Park","year":"2014","journal-title":"PLOS Pathog."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib95","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/prot.21135","article-title":"Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks","volume":"65","author":"Passerini","year":"2006","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib96","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/B978-0-12-800128-8.00001-7","article-title":"Carbohydrate-protein interactions: Molecular modeling insights","volume":"71","author":"Perez","year":"2014","journal-title":"Adv. Carbohydr. Chem. Biochem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib97","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1007\/s10719-017-9766-7","article-title":"Insights into the effects of glycosylation and the monosaccharide-binding activity of the plant lectin CrataBL","volume":"34","author":"Pol-Fachin","year":"2017","journal-title":"Glycoconj. J."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib98","article-title":"Glycoarray technologies: Deciphering interactions from proteins to live cell responses","volume":"5","author":"Puvirajesinghe","year":"2016","journal-title":"Microarrays (Basel)"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib99","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1351\/pac198961071293","article-title":"Protein-carbohydrate interactions: Basic molecular features","volume":"61","author":"Quiocho","year":"1989","journal-title":"Pure Appl. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib100","doi-asserted-by":"crossref","first-page":"3411","DOI":"10.1039\/b822877a","article-title":"Carbohydrate-aromatic pi interactions: A test of density functionals and the DFT-D method","volume":"11","author":"Raju","year":"2009","journal-title":"Phys. Chem. Chem. Phys."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib1010","doi-asserted-by":"crossref","first-page":"2743","DOI":"10.1039\/b802144a","article-title":"Docking, synthesis, and NMR studies of mannosyl trisaccharide ligands for DC-SIGN lectin","volume":"6","author":"Reina","year":"2008","journal-title":"Org. Biomol. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib101","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1007\/s10822-011-9433-1","article-title":"Docking glycosaminoglycans to proteins: Analysis of solvent inclusion","volume":"25","author":"Samsonov","year":"2011","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib102","doi-asserted-by":"crossref","first-page":"E5312","DOI":"10.1073\/pnas.1412703111","article-title":"The cholesterol-dependent cytolysins pneumolysin and streptolysin O require binding to red blood cell glycans for hemolytic activity","volume":"111","author":"Shewell","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib103","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1093\/protein\/gzg065","article-title":"An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins","volume":"16","author":"Shionyu-Mitsuyama","year":"2003","journal-title":"Protein Eng."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib104","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1093\/bioinformatics\/btm618","article-title":"Prediction of zinc-binding sites in proteins from sequence","volume":"24","author":"Shu","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib105","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1007\/s10822-005-9033-z","article-title":"Modelling of carbohydrate-aromatic interactions: Ab initio energetics and force field performance","volume":"19","author":"Spiwok","year":"2005","journal-title":"J. Comput. Aided Mol. Des."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib106","doi-asserted-by":"crossref","DOI":"10.3390\/molecules22071038","article-title":"CH\/pi interactions in carbohydrate recognition","volume":"22","author":"Spiwok","year":"2017","journal-title":"Molecules"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib107","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1002\/prot.10612","article-title":"Identification of common structural features of binding sites in galactose-specific proteins","volume":"55","author":"Sujatha","year":"2004","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib108","doi-asserted-by":"crossref","first-page":"843030","DOI":"10.1155\/2015\/843030","article-title":"Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information","volume":"2015","author":"Suresh","year":"2015","journal-title":"Adv. Bioinform."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib109","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1021\/acs.jcim.6b00320","article-title":"Sequence-based prediction of protein-carbohydrate binding sites using support vector machines","volume":"56","author":"Taherzadeh","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib110","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1021\/ct700029q","article-title":"Prediction of the structure of complexes comprised of proteins and glycosaminoglycans using docking simulation and cluster analysis","volume":"3","author":"Takaoka","year":"2007","journal-title":"J. Chem. Theory Comput."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib111","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1093\/protein\/13.2.89","article-title":"Analysis and prediction of carbohydrate binding sites","volume":"13","author":"Taroni","year":"2000","journal-title":"Protein Eng."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib112","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1080\/08927020701710890","article-title":"Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids","volume":"34","author":"Tessier","year":"2008","journal-title":"Mol. Simul."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib113","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib114","doi-asserted-by":"crossref","first-page":"e40846","DOI":"10.1371\/journal.pone.0040846","article-title":"Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms","volume":"7","author":"Tsai","year":"2012","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib115","doi-asserted-by":"crossref","first-page":"7570","DOI":"10.1002\/chem.200800247","article-title":"Aromatic-carbohydrate interactions: An NMR and computational study of model systems","volume":"14","author":"Vandenbussche","year":"2008","journal-title":"Chemistry"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib116","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/prot.10465","article-title":"Improved protein-ligand docking using GOLD","volume":"52","author":"Verdonk","year":"2003","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib117","doi-asserted-by":"crossref","first-page":"692738","DOI":"10.1155\/2014\/692738","article-title":"Molecular dynamics and metadynamics simulations of the cellulase Cel48F","volume":"2014","author":"Vital De Oliveira","year":"2014","journal-title":"Enzyme Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib118","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.jmgm.2016.10.018","article-title":"Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies","volume":"71","author":"Walker","year":"2017","journal-title":"J. Mol. Graph. Model."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib119","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/nbt0302-275","article-title":"Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells","volume":"20","author":"Wang","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib120","doi-asserted-by":"crossref","first-page":"W243","DOI":"10.1093\/nar\/gkl298","article-title":"BindN: A web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences","volume":"34","author":"Wang","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib121","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.carres.2014.10.028","article-title":"Force fields and scoring functions for carbohydrate simulation","volume":"401","author":"Xiong","year":"2015","journal-title":"Carbohydr. Res."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib122","doi-asserted-by":"crossref","first-page":"2080","DOI":"10.1002\/prot.24100","article-title":"A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction","volume":"80","author":"Yang","year":"2012","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib123","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1110\/ps.033480.107","article-title":"Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions","volume":"17","author":"Yang","year":"2008","journal-title":"Protein Sci."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib124","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s13361-015-1263-2","article-title":"Localizing carbohydrate binding sites in proteins using hydrogen\/deuterium exchange mass spectrometry","volume":"27","author":"Zhang","year":"2016","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib125","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1002\/jcc.23730","article-title":"Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction","volume":"35","author":"Zhao","year":"2014","journal-title":"J. Comput. Chem."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib126","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1110\/ps.0217002","article-title":"Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction","volume":"11","author":"Zhou","year":"2002","journal-title":"Protein Sci."},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib127","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1002\/prot.1099","article-title":"Prediction of protein interaction sites from sequence profile and residue neighbor list","volume":"44","author":"Zhou","year":"2001","journal-title":"Proteins"},{"key":"10.1016\/B978-0-12-809633-8.20661-4_bib128","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/0022-2836(87)90501-8","article-title":"Prediction of protein secondary structure and active sites using the alignment of homologous sequences","volume":"195","author":"Zvelebil","year":"1987","journal-title":"J. Mol. Biol."}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338206614?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338206614?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T21:40:45Z","timestamp":1720302045000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338206614"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":131,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20661-4","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}