{"id":"https://openalex.org/W641640508","doi":null,"title":"Biomolecular simulations : methods and protocols","display_name":"Biomolecular simulations : methods and protocols","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W641640508","mag":"641640508"},"language":"en","primary_location":{"id":"mag:641640508","doi":null,"is_oa":false,"landing_page_url":"http://perpus.biotek.lipi.go.id/index.php?p=show_detail&id=15364&keywords=","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Humana Press eBooks","raw_type":null},"volume":null,"type":"book","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083958570","display_name":"Luca Monticelli","orcid":"https://orcid.org/0000-0002-6352-4595","observed_orcids":["https://orcid.org/0000-0002-6352-4595"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luca Monticelli","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6352-4595","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5111781190","display_name":"Emppu Salonen","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Emppu Salonen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.3366,"has_fulltext":false,"cited_by_count":171,"citation_normalized_percentile":{"value":0.91558442,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8838000297546387,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8838000297546387,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.07590000331401825,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.020500000566244125,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biomolecular-simulation","display_name":"biomolecular simulation","score":0.8090000152587891},{"id":"https://openalex.org/keywords/quantum-mechanics-calculations","display_name":"quantum mechanics calculations","score":0.6489999890327454},{"id":"https://openalex.org/keywords/density-functional-theory","display_name":"density functional theory","score":0.7789999842643738},{"id":"https://openalex.org/keywords/ab-initio-molecular-dynamics","display_name":"ab initio molecular dynamics","score":0.9440000057220459},{"id":"https://openalex.org/keywords/qm-mm","display_name":"QM/MM","score":0.9039999842643738},{"id":"https://openalex.org/keywords/classical-molecular-dynamics","display_name":"classical molecular dynamics","score":0.8930000066757202},{"id":"https://openalex.org/keywords/enhanced-sampling","display_name":"enhanced sampling","score":0.8339999914169312},{"id":"https://openalex.org/keywords/force-fields","display_name":"force fields","score":0.9700000286102295},{"id":"https://openalex.org/keywords/polarizable-force-field","display_name":"polarizable force field","score":0.996999979019165},{"id":"https://openalex.org/keywords/electrostatics","display_name":"electrostatics","score":0.8640000224113464},{"id":"https://openalex.org/keywords/free-energy-calculations","display_name":"free energy calculation","score":0.9929999709129333},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.9950000047683716},{"id":"https://openalex.org/keywords/membrane-transporters","display_name":"membrane transporters","score":0.9860000014305115},{"id":"https://openalex.org/keywords/lipid-bilayers","display_name":"lipid bilayers","score":0.9890000224113464},{"id":"https://openalex.org/keywords/lipid-monolayers","display_name":"lipid monolayers","score":0.9990000128746033},{"id":"https://openalex.org/keywords/coarse-grained-models","display_name":"coarse-grained models","score":0.8769999742507935},{"id":"https://openalex.org/keywords/martini-force-field","display_name":"Martini force field","score":0.9079999923706055}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7946306467056274},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4854181706905365},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4665023684501648},{"id":"https://openalex.org/C139287275","wikidata":"https://www.wikidata.org/wiki/Q869891","display_name":"Polarizability","level":3,"score":0.4654572308063507},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.4326740503311157},{"id":"https://openalex.org/C152365726","wikidata":"https://www.wikidata.org/wiki/Q1048589","display_name":"Density functional theory","level":2,"score":0.41982796788215637},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.41850173473358154},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.4122544527053833},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4049531817436218},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.20018985867500305},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.15216124057769775}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:641640508","doi":null,"is_oa":false,"landing_page_url":"http://perpus.biotek.lipi.go.id/index.php?p=show_detail&id=15364&keywords=","pdf_url":null,"source":{"id":"https://openalex.org/S4306463399","display_name":"Humana Press eBooks","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/P4310315801","host_organization_name":"Humana Press","host_organization_lineage":["https://openalex.org/P4310315801","https://openalex.org/P4310319900"],"host_organization_lineage_names":["Humana Press","Springer Science+Business Media"],"type":"ebook platform"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Humana Press eBooks","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2303493384","https://openalex.org/W2905304269","https://openalex.org/W2942689596","https://openalex.org/W2996385237","https://openalex.org/W2603102037","https://openalex.org/W7208813916","https://openalex.org/W3082179753","https://openalex.org/W2339608274","https://openalex.org/W4247056313","https://openalex.org/W7065855396"],"abstract_inverted_index":{"Part":[0,59,262],"I:":[1],"Quantum":[2],"Mechanics":[3],"Calculations":[4,13,131,144],"1.":[5],"Ab":[6,25],"initio,":[7],"Density":[8],"Functional":[9],"Theory,":[10],"and":[11,21,43,49,56,82,94,105,119,135,154,168,193,212,222,234,241,259,266,297,307,316,342,348],"Semi-empirical":[12],"Mikael":[14],"P.":[15],"Johansson,":[16],"Ville":[17],"R.":[18,133],"I.":[19],"Kaila":[20],"Dage":[22],"Sundholm":[23],"2.":[24],"initio":[26],"Molecular":[27,67,90,158,197,230,249,293,334],"Dynamics":[28,68,91,198,252,327,335],"Kari":[29],"Laasonen":[30],"3.":[31],"Introduction":[32,124,323],"to":[33,125,207,251,324],"QM/MM":[34,50],"simulations":[35,113],"Gerrit":[36],"Groenhof":[37],"4.":[38],"Computational":[39],"Enzymology":[40],"Alessio":[41],"Lodola":[42],"Adrian":[44],"J.":[45],"Mulholland":[46],"5.":[47],"QM":[48],"Simulations":[51,64,199,216,265,336,352],"of":[52,174,177,200,205,217,246,337],"Proteins":[53,339],"Thomas":[54],"Steinbrecher":[55],"Marcus":[57],"Elstner":[58],"II:":[60],"Classical":[61,66,89],"Mechanics:":[62],"Atomistic":[63],"6.":[65],"in":[69,111,128,145,253],"a":[70],"Nutshell":[71],"Susanna":[72],"Hug":[73],"7.":[74],"Enhanced":[75],"Sampling":[76],"Algorithms":[77],"Ayori":[78],"Mitsutake,":[79],"Yoshiharu":[80],"Mori,":[81],"Yuko":[83],"Okamoto":[84],"8.":[85],"Force":[86,100,284],"Fields":[87,101],"for":[88,141,272,304],"Luca":[92],"Monticelli":[93],"D.":[95,223],"Peter":[96,224,343],"Tieleman":[97,225],"9.":[98],"Polarizable":[99],"Hanne":[102],"S.":[103,166],"Antila":[104],"Emppu":[106],"Salonen":[107],"10.":[108],"Electrostatics":[109],"interactions":[110],"classical":[112],"G.":[114,278],"Andres":[115],"Cisneros,":[116],"Volodymyr":[117,150],"Babin,":[118,151],"Celeste":[120,152],"Sagui":[121],"11.":[122],"An":[123,322],"Best":[126],"Practices":[127],"Free":[129,142],"Energy":[130,143],"Michael":[132],"Shirts":[134],"David":[136],"L.":[137],"Mobley":[138],"12.":[139],"Recipes":[140],"Biomolecular":[146],"Systems":[147],"Mahmoud":[148],"Moradi,":[149],"Sagui,":[153],"Christopher":[155],"Roland":[156],"13.":[157],"Docking":[159,250],"Methodologies":[160],"Andrea":[161],"Bortolato,":[162],"Marco":[163],"Fanton,":[164],"Jonathan":[165],"Mason":[167],"Stefano":[169],"Moro":[170],"14.":[171],"Simulation":[172,245],"Studies":[173],"the":[175],"Mechanism":[176],"Membrane":[178,338],"Transporters":[179],"Giray":[180],"Enkavi,":[181],"Jing":[182],"Li,":[183],"Paween":[184],"Mahinthichaichan,":[185],"Po-Chao":[186],"Wen,":[187],"Zhijian":[188],"Huang,":[189],"Saher":[190],"A.":[191],"Shaikh":[192],"Emad":[194],"Tajkhorshid":[195],"15.":[196],"Lipid":[201,218],"Bilayers:":[202],"Simple":[203],"Recipe":[204],"How":[206],"Do":[208],"It":[209],"Hector":[210],"Martinez-Seara":[211],"Tomasz":[213],"Rog":[214],"16.":[215],"Monolayers":[219],"Svetlana":[220],"Baoukina":[221],"17.":[226],"Simulating":[227],"DNA":[228],"by":[229],"Dynamics:":[231],"Aims,":[232],"Methods,":[233],"Validation":[235],"Nicolas":[236,255],"Foloppe":[237],",":[238],"Marc":[239],"Gueroult":[240],"Brigitte":[242],"Hartmann":[243],"18.":[244],"Carbohydrates,":[247],"From":[248],"Water":[254],"Sapay,":[256],"Alessandra":[257],"Nurisso":[258],"Anne":[260],"Imberty":[261],"III:":[263],"Mesoscopic":[264],"Coarse-grained":[267,275,302,351],"Models":[268,276,303],"19.":[269],"Systematic":[270],"Methods":[271],"Structurally":[273],"Consistent":[274],"W.":[277],"Noid":[279],"20.":[280],"The":[281],"Martini":[282],"Coarse-Grained":[283],"Field":[285],"Siewert-Jan":[286],"Marrink":[287],"&":[288],"Xavier":[289],"Periole":[290],"21.":[291],"Multiscale":[292,333],"Modeling":[294],"Matej":[295],"Praprotnik":[296],"Luigi":[298],"Delle":[299],"Site":[300],"22.":[301],"Protein":[305],"Folding":[306],"Aggregation":[308],"Philippe":[309],"Derreumaux":[310],"23.":[311],"Elastic":[312],"Network":[313],"Models:":[314],"Theoretical":[315],"Empirical":[317],"Foundations":[318],"Yves-Henri":[319],"Sanejouand":[320],"24.":[321],"Dissipative":[325],"Particle":[326],"Zhong-Yuan":[328],"Lu,":[329],"Yong-Lei":[330],"Wang":[331],"25.":[332],"Syma":[340],"Khalid":[341],"J":[344],"Bond":[345],"26.":[346],"Vesicles":[347],"Vesicle":[349],"Fusion:":[350],"Julian":[353],"C":[354],"Shillcock":[355]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":44},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
