{"id":"https://openalex.org/W4238599669","doi":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","title":"Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas","display_name":"Neighbor-list reduction: Optimization for computation of molecular van der Waals and solvent-accessible surface areas","publication_year":1998,"publication_date":"1998-05-01","ids":{"openalex":"https://openalex.org/W4238599669","doi":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","is_oa":true,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/%28SICI%291096-987X%28199805%2919%3A7%3C797%3A%3AAID-JCC9%3E3.0.CO%3B2-L","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/%28SICI%291096-987X%28199805%2919%3A7%3C797%3A%3AAID-JCC9%3E3.0.CO%3B2-L","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109119581","display_name":"J\ufffdrg Weiser","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J\ufffdrg Weiser","raw_affiliation_strings":["Department of Chemistry, Columbia University, New York, New York 10027"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Columbia University, New York, New York 10027","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045677312","display_name":"Armin A. Weiser","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Armin A. Weiser","raw_affiliation_strings":["Department of Chemistry, Columbia University, New York, New York 10027"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Columbia University, New York, New York 10027","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055000783","display_name":"Peter S. Shenkin","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter S. Shenkin","raw_affiliation_strings":["Department of Chemistry, Columbia University, New York, New York 10027"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Columbia University, New York, New York 10027","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062779702","display_name":"W. Clark Still","orcid":null},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. Clark Still","raw_affiliation_strings":["Department of Chemistry, Columbia University, New York, New York 10027"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Columbia University, New York, New York 10027","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5109119581"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":2.2507,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.88185756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"7","first_page":"797","last_page":"808"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12285","display_name":"Surface Chemistry and Catalysis","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sasa","display_name":"Sasa","score":0.8540781736373901},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6872437596321106},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.65395587682724},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.5903701186180115},{"id":"https://openalex.org/keywords/accessible-surface-area","display_name":"Accessible surface area","score":0.5770441293716431},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.5636111497879028},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5477518439292908},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.5247833132743835},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.5067740082740784},{"id":"https://openalex.org/keywords/van-der-waals-radius","display_name":"Van der Waals radius","score":0.466705322265625},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.43165791034698486},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4148949384689331},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4001503884792328},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34555500745773315},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.3389163613319397},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32114410400390625},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.31713375449180603},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3136030435562134},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.2395119071006775},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.15683934092521667},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.13495036959648132}],"concepts":[{"id":"https://openalex.org/C2776335000","wikidata":"https://www.wikidata.org/wiki/Q2322484","display_name":"Sasa","level":2,"score":0.8540781736373901},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6872437596321106},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.65395587682724},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.5903701186180115},{"id":"https://openalex.org/C11072593","wikidata":"https://www.wikidata.org/wiki/Q3622068","display_name":"Accessible surface area","level":2,"score":0.5770441293716431},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.5636111497879028},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5477518439292908},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.5247833132743835},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.5067740082740784},{"id":"https://openalex.org/C73683733","wikidata":"https://www.wikidata.org/wiki/Q166879","display_name":"Van der Waals radius","level":4,"score":0.466705322265625},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.43165791034698486},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4148949384689331},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4001503884792328},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34555500745773315},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.3389163613319397},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32114410400390625},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.31713375449180603},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3136030435562134},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.2395119071006775},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.15683934092521667},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.13495036959648132},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","is_oa":true,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/%28SICI%291096-987X%28199805%2919%3A7%3C797%3A%3AAID-JCC9%3E3.0.CO%3B2-L","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","is_oa":true,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199805)19:7<797::aid-jcc9>3.0.co;2-l","pdf_url":"https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/%28SICI%291096-987X%28199805%2919%3A7%3C797%3A%3AAID-JCC9%3E3.0.CO%3B2-L","source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4238599669.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W59526888","https://openalex.org/W1966041739","https://openalex.org/W1989906898","https://openalex.org/W2001900040","https://openalex.org/W2003399913","https://openalex.org/W2004360551","https://openalex.org/W2005651680","https://openalex.org/W2008708467","https://openalex.org/W2014612057","https://openalex.org/W2018392691","https://openalex.org/W2023455361","https://openalex.org/W2024243556","https://openalex.org/W2027491603","https://openalex.org/W2029087609","https://openalex.org/W2030256857","https://openalex.org/W2040446474","https://openalex.org/W2040950615","https://openalex.org/W2044010751","https://openalex.org/W2065232574","https://openalex.org/W2072073580","https://openalex.org/W2087179087","https://openalex.org/W2095375069","https://openalex.org/W2111018312","https://openalex.org/W2116064497","https://openalex.org/W2122410355","https://openalex.org/W2131124255","https://openalex.org/W2132456736","https://openalex.org/W2144659448","https://openalex.org/W2162627883","https://openalex.org/W2167404361","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W1969178306","https://openalex.org/W2040181313","https://openalex.org/W2079679729","https://openalex.org/W2022450294","https://openalex.org/W2313553391","https://openalex.org/W2090387874","https://openalex.org/W2094068045","https://openalex.org/W2099246483","https://openalex.org/W1974033720","https://openalex.org/W2045983332"],"abstract_inverted_index":{"A":[0],"general,":[1],"fast,":[2],"and":[3,107,121,139,153,156,237],"exact":[4],"optimization,":[5],"called":[6],"neighbor-list":[7,91],"reduction":[8,191],"(NLR),":[9],"is":[10,166,188,192,205,215],"presented,":[11],"which":[12,136],"can":[13],"be":[14,34,242],"used":[15,148],"to":[16,33,52,202,241,244,248],"accelerate":[17],"the":[18,37,45,48,68,80,103,119,133,168,172,175,190,219,224],"computation":[19,38,220],"of":[20,29,47,58,75,90,123,128,132,150,174,208,221,226],"hard-sphere":[21],"molecular":[22,140],"surface":[23,50,141,164,185,234],"areas.":[24],"NLR":[25,169],"allows":[26],"selected":[27],"neighbors":[28],"a":[30,40,55,99,129,206],"central":[31,69,81,101],"atom":[32,70],"removed":[35,62],"from":[36],"in":[39,223],"preprocessing":[41],"step,":[42],"thus":[43],"allowing":[44],"calculation":[46],"atom's":[49],"area":[51,186],"proceed":[53],"with":[54,67,79,155],"shorter":[56],"list":[57,177],"neighbors.":[59,116],"The":[60,197],"atoms":[61],"are":[63],"those":[64,249],"having":[65],"intersections":[66,78],"falling":[71],"entirely":[72],"within":[73,245],"unions":[74],"other":[76,109,115],"atoms'":[77],"atom.":[82],"We":[83,117],"describe":[84],"explicit":[85,158],"methods":[86,170],"for":[87,105,212,218],"two":[88,114],"levels":[89],"reduction:":[92],"3NLR":[93],"considers":[94,113],"three":[95],"hard":[96],"spheres":[97],"at":[98],"time\u2014the":[100],"atom,":[102],"candidate":[104],"removal,":[106],"one":[108],"neighbor;":[110],"whereas":[111],"4NLR":[112],"demonstrate":[118],"correctness":[120],"efficiency":[122],"this":[124,227],"optimization":[125],"by":[126,178],"means":[127],"modified":[130],"version":[131],"NACCESS":[134],"program,":[135],"computes":[137],"atomic":[138,233],"areas":[142,235],"numerically.":[143],"As":[144],"test":[145],"cases":[146],"we":[147],"compounds":[149],"different":[151],"size":[152],"class,":[154],"without":[157,251],"hydrogens.":[159],"When":[160],"van":[161],"der":[162],"Waals":[163],"(vdWSA)":[165],"computed,":[167,189],"reduce":[171],"length":[173],"neighbor":[176],"as":[179,181,193,195],"much":[180],"41%;":[182],"when":[183],"solvent-accessible":[184],"(SASA)":[187],"great":[194],"74%.":[196],"overall":[198],"speed":[199],"improvement":[200],"due":[201],"these":[203],"reductions":[204],"factor":[207],"only":[209],"about":[210,216],"1.2":[211],"vdWSA,":[213],"but":[214],"2.0":[217],"SASA,":[222],"context":[225],"particular":[228],"program.":[229],"All":[230],"39,554":[231],"calculated":[232],"(vdWSA":[236],"SASA)":[238],"were":[239],"found":[240],"identical":[243],"0.001":[246],"\u00c52":[247],"obtained":[250],"NLR.":[252],"\u00a9":[253],"1998":[254,265],"John":[255],"Wiley":[256],"&":[257],"Sons,":[258],"Inc.":[259],"J":[260],"Comput":[261],"Chem":[262],"19:":[263],"797\u2013808,":[264]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}