{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T21:08:28Z","timestamp":1773004108114,"version":"3.50.1"},"reference-count":45,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2020,11,1]],"date-time":"2020-11-01T00:00:00Z","timestamp":1604188800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,11,1]],"date-time":"2020-11-01T00:00:00Z","timestamp":1604188800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"DOI":"10.13039\/501100007421","name":"University of the Philippines","doi-asserted-by":"publisher","award":["151512 PNSE"],"award-info":[{"award-number":["151512 PNSE"]}],"id":[{"id":"10.13039\/501100007421","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Graphics and Modelling"],"published-print":{"date-parts":[[2020,11]]},"DOI":"10.1016\/j.jmgm.2020.107657","type":"journal-article","created":{"date-parts":[[2020,6,24]],"date-time":"2020-06-24T12:08:19Z","timestamp":1593000499000},"page":"107657","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":11,"special_numbering":"C","title":["Computational reverse engineering of the lipase from Pseudomonas aeruginosa PAO1: \u03b1-helices"],"prefix":"10.1016","volume":"100","author":[{"given":"Adam Jo J.","family":"Elatico","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricky B.","family":"Nellas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmgm.2020.107657_bib1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2014\/684506","article-title":"From structure to catalysis: recent developments in the biotechnological applications of lipases","volume":"2014","author":"Anobom","year":"2014","journal-title":"BioMed Res. Int."},{"key":"10.1016\/j.jmgm.2020.107657_bib2","first-page":"575","article-title":"The lipases","volume":"vol. 7","author":"Desnuelle","year":"1972"},{"key":"10.1016\/j.jmgm.2020.107657_bib3","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/S0734-9750(01)00086-6","article-title":"Production, purification, characterization, and applications of lipases","volume":"19","author":"Sharma","year":"2001","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.jmgm.2020.107657_bib4","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1016\/S0167-7799(98)01195-0","article-title":"Microbial lipases form versatile tools for biotechnology","volume":"16","author":"Jaeger","year":"1998","journal-title":"Trends Biotechnol."},{"key":"10.1016\/j.jmgm.2020.107657_bib5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.enzmictec.2005.10.016","article-title":"Industrial applications of microbial lipases","volume":"39","author":"Hasan","year":"2006","journal-title":"Enzym. Microb. Technol."},{"key":"10.1016\/j.jmgm.2020.107657_bib6","first-page":"125","article-title":"A\u00a0novel low-temperature resistant alkaline lipase from a soda lake fungus strain Fusarium solani N4-2 for detergent formulation","volume":"76","author":"Liu","year":"2012","journal-title":"J.\u00a0Mol. Catal. B Enzym."},{"key":"10.1016\/j.jmgm.2020.107657_bib7","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1007\/s11746-999-0067-6","article-title":"Conversion of vegetable oil to biodiesel using immobilized Candida Antarctica lipase","volume":"76","author":"Shimada","year":"1999","journal-title":"JAOCS (J. Am. Oil Chem. Soc.)"},{"key":"10.1016\/j.jmgm.2020.107657_bib8","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/S0960-8524(01)00203-6","article-title":"Immobilized Candida Antarctica lipase-catalyzed alcoholysis of cotton seed oil in a solvent-free medium","volume":"83","author":"Kose","year":"2002","journal-title":"Bioresour. Technol."},{"key":"10.1016\/j.jmgm.2020.107657_bib9","series-title":"Advances in Enzyme Technology","first-page":"484","article-title":"Thermostable enzymes for industrial biotechnology","author":"Sharma","year":"2019"},{"key":"10.1016\/j.jmgm.2020.107657_bib10","article-title":"Lipase improvement: goals and strategies","volume":"2","author":"Bassegoda","year":"2012","journal-title":"Computational and Structural Biotechnology"},{"key":"10.1016\/j.jmgm.2020.107657_bib11","doi-asserted-by":"crossref","DOI":"10.1038\/srep10654","article-title":"Economical analysis of saturation mutagenesis experiments","volume":"5","author":"Acevedo-Rocha","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jmgm.2020.107657_bib12","doi-asserted-by":"crossref","first-page":"2948","DOI":"10.1111\/febs.12324","article-title":"Computational design gains momentum in enzyme catalysis engineering","volume":"280","author":"Wijma","year":"2013","journal-title":"FEBS J."},{"key":"10.1016\/j.jmgm.2020.107657_bib13","doi-asserted-by":"crossref","first-page":"31219","DOI":"10.1074\/jbc.M003903200","article-title":"Crystal structure of Pseudomonas aeruginosa lipase in the open conformation","volume":"275","author":"Nardini","year":"2000","journal-title":"J.\u00a0Biol. Chem."},{"issue":"16","key":"10.1016\/j.jmgm.2020.107657_bib14","article-title":"The lid domain in lipases: structural and functional determinant of enzymatic properties","volume":"5","author":"Khan","year":"2017","journal-title":"Frontiers in Bioengineering and Biotechnology"},{"key":"10.1016\/j.jmgm.2020.107657_bib15","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1039\/C4CC08477B","article-title":"Saturation mutagenesis in selected amino acids to shift Pseudomonas sp. acidic lipase Lip I.3 substrate specificity and activity","volume":"51","author":"Panizza","year":"2014","journal-title":"Chem. Commun."},{"key":"10.1016\/j.jmgm.2020.107657_bib16","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.molcatb.2009.06.006","article-title":"The effect of substitution of Phe181 and Phe182 with Ala on activity, substrate specificity and stabilization of substrate at the active site of Bacillus thermocatenulatus lipase","volume":"61","author":"Karkhane","year":"2009","journal-title":"J.\u00a0Mol. Catal. B Enzym."},{"key":"10.1016\/j.jmgm.2020.107657_bib17","doi-asserted-by":"crossref","first-page":"25396","DOI":"10.1074\/jbc.270.43.25396","article-title":"Human hepatic and lipoprotein lipase: the loop covering the catalytic site mediates lipase substrate specificity","volume":"270","author":"Dugi","year":"1995","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jmgm.2020.107657_bib18","doi-asserted-by":"crossref","first-page":"2312","DOI":"10.1110\/ps.0304003","article-title":"Sequence of the lid affects activity and specificity of Candida rugosa lipase isoenzymes","volume":"12","author":"Brocca","year":"2009","journal-title":"Protein Sci."},{"key":"10.1016\/j.jmgm.2020.107657_bib19","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1016\/j.febslet.2005.03.037","article-title":"Mutations in the \u2013lid\" region affect chain length specificity and thermostability of a Pseudomonas fragi lipase","volume":"i","author":"Santarossa","year":"2005","journal-title":"FEBS (Fed. Eur. Biochem. Soc.) Lett."},{"key":"10.1016\/j.jmgm.2020.107657_bib20","article-title":"Engineering a disulfide bond in the lid hinge region of Rhizopus chinensis lipase: increased thermostability and altered acyl chain length specificity","volume":"7","author":"Yu","year":"2012","journal-title":"PloS One"},{"key":"10.1016\/j.jmgm.2020.107657_bib21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0085186","article-title":"The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases","volume":"8","author":"Timucin","year":"2013","journal-title":"PloS One"},{"key":"10.1016\/j.jmgm.2020.107657_bib22","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.4014\/jmb.1506.06011","article-title":"Characterizing LipR from Pseudomonas sp. R0-14 and applying in enrichment of polyunsaturated fatty acids from algal oil","volume":"25","author":"Yang","year":"2015","journal-title":"J.\u00a0Microbiol. Biotechnol."},{"key":"10.1016\/j.jmgm.2020.107657_bib23","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1128\/AEM.03371-13","article-title":"Protein engineering by random mutagenesis and structure- guided consensus of geobacillus stearothermophilus lipase T6 for enhanced stability in methanol","volume":"80","author":"Dror","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.jmgm.2020.107657_bib24","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1007\/s12010-013-0209-z","article-title":"Role of Met93 and Thr96 in the lid hinge region of rhizopus chinensis lipase","volume":"170","author":"Zhu","year":"2013","journal-title":"Appl. Biochem. Biotechnol."},{"key":"10.1016\/j.jmgm.2020.107657_bib25","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s10529-009-0121-3","article-title":"Residue Tyr224 is critical for the thermostability of Geobacillus sp. RD-2 lipase","volume":"32","author":"Wu","year":"2010","journal-title":"Biotechnol. Lett."},{"key":"10.1016\/j.jmgm.2020.107657_bib26","doi-asserted-by":"crossref","first-page":"6238","DOI":"10.1021\/bi300557y","article-title":"Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa","volume":"51","author":"Johnson","year":"2012","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmgm.2020.107657_bib27","doi-asserted-by":"crossref","first-page":"e28","DOI":"10.1371\/journal.pcbi.0010028","article-title":"Evidence of a double- lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations","volume":"1","author":"Cherukuvada","year":"2005","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jmgm.2020.107657_bib28","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1042\/bj2970249","article-title":"The structure and function of proline-rich regions in proteins","volume":"297","author":"Williamson","year":"1994","journal-title":"Biochem. J."},{"key":"10.1016\/j.jmgm.2020.107657_bib29","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmgm.2020.107657_bib30","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jmgm.2020.107657_bib31","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J.\u00a0Chem. Theor. Comput."},{"key":"10.1016\/j.jmgm.2020.107657_bib32","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"10.1016\/j.jmgm.2020.107657_bib33","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jmgm.2020.107657_bib34","doi-asserted-by":"crossref","first-page":"9020","DOI":"10.1021\/jp8001614","article-title":"Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations","volume":"112","author":"Joung","year":"2008","journal-title":"J.\u00a0Phys. Chem. B"},{"key":"10.1016\/j.jmgm.2020.107657_bib35","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jmgm.2020.107657_bib36","doi-asserted-by":"crossref","first-page":"2375","DOI":"10.1063\/1.432526","article-title":"Generalized Langevin equation approach for atom\/solid - surface scattering: general formulation for classical scattering off harmonic solids","volume":"64","author":"Adelman","year":"1976","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jmgm.2020.107657_bib37","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald: an N.log(N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J.\u00a0Chem. Phys."},{"key":"10.1016\/j.jmgm.2020.107657_bib38","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J.\u00a0Comput. Phys."},{"key":"10.1016\/j.jmgm.2020.107657_bib39","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"J.\u00a0Chem. Theor. Comput."},{"key":"10.1016\/j.jmgm.2020.107657_bib40","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1016\/S0263-7855(97)00009-X","article-title":"HOLE: a program for the analysis of the pore dimensions of ion channel structural models","volume":"14","author":"Smart","year":"1996","journal-title":"J.\u00a0Mol. Graph."},{"key":"10.1016\/j.jmgm.2020.107657_bib41","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1021\/ja00315a051","article-title":"A\u00a0new force field for molecular mechanical simulation of nucleic acids and proteins","volume":"106","author":"Weiner","year":"1984","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.jmgm.2020.107657_bib42","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1093\/protein\/gzl007","article-title":"Generation and analysis of proline mutants in protein G. Protein Engineering","volume":"19","author":"Choi","year":"2006","journal-title":"Design and Selection"},{"key":"10.1016\/j.jmgm.2020.107657_bib43","series-title":"Protein Engineering","first-page":"69","article-title":"A\u00a0computational library design protocol for rapid improve ment of protein stability: fresco","volume":"vol. 1685","author":"Wijma","year":"2017"},{"key":"10.1016\/j.jmgm.2020.107657_bib44","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/s41589-018-0053-0","article-title":"Computational redesign of enzymes for regio- and enantioselective hydroamination","volume":"14","author":"Li","year":"2018","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.jmgm.2020.107657_bib45","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera \u2013 a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J.\u00a0Comput. Chem."}],"container-title":["Journal of Molecular Graphics and Modelling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326320304460?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326320304460?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T21:06:20Z","timestamp":1761080780000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1093326320304460"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11]]},"references-count":45,"alternative-id":["S1093326320304460"],"URL":"https:\/\/doi.org\/10.1016\/j.jmgm.2020.107657","relation":{},"ISSN":["1093-3263"],"issn-type":[{"value":"1093-3263","type":"print"}],"subject":[],"published":{"date-parts":[[2020,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Computational reverse engineering of the lipase from Pseudomonas aeruginosa PAO1: \u03b1-helices","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Graphics and Modelling","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmgm.2020.107657","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"107657"}}