Ontology type: schema:ScholarlyArticle
2012-02
AUTHORSOlexandr Ya Yakovenko, Yvonne Y. Li, Alexander A. Oliferenko, Ganna M. Vashchenko, Volodymyr G. Bdzhola, Steven J. M. Jones
ABSTRACTThe YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds. More... »
PAGES663-673
http://scigraph.springernature.com/pub.10.1007/s00894-011-1095-3
DOIhttp://dx.doi.org/10.1007/s00894-011-1095-3
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1024365866
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/21562826
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0306",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Physical Chemistry (incl. Structural)",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/03",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Chemical Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Algorithms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cations",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Computer Simulation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Drug Design",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Models, Molecular",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Reproducibility of Results",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Yakovenko",
"givenName": "Olexandr Ya",
"type": "Person"
},
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Li",
"givenName": "Yvonne Y.",
"id": "sg:person.01271473750.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01271473750.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Florida",
"id": "https://www.grid.ac/institutes/grid.15276.37",
"name": [
"Department of Chemistry, University of Florida, 32611, Gainesville, FL, USA"
],
"type": "Organization"
},
"familyName": "Oliferenko",
"givenName": "Alexander A.",
"id": "sg:person.01003164525.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003164525.16"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of British Columbia",
"id": "https://www.grid.ac/institutes/grid.17091.3e",
"name": [
"Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Vashchenko",
"givenName": "Ganna M.",
"id": "sg:person.0737135336.45",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0737135336.45"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Institute of Molecular Biology and Genetics",
"id": "https://www.grid.ac/institutes/grid.418824.3",
"name": [
"Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, 150 Zabolotny str, 03143, Kyiv, Ukraine"
],
"type": "Organization"
},
"familyName": "Bdzhola",
"givenName": "Volodymyr G.",
"id": "sg:person.01077471235.75",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01077471235.75"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BC Cancer Agency",
"id": "https://www.grid.ac/institutes/grid.248762.d",
"name": [
"Genome Sciences Centre, BC Cancer Agency, Suite 100 570 West 7th Avenue, Vancouver, British Columbia, Canada"
],
"type": "Organization"
},
"familyName": "Jones",
"givenName": "Steven J. M.",
"id": "sg:person.011076371162.80",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011076371162.80"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1007/s00894-009-0572-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003660229",
"https://doi.org/10.1007/s00894-009-0572-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00894-009-0572-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003660229",
"https://doi.org/10.1007/s00894-009-0572-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00894-009-0572-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003660229",
"https://doi.org/10.1007/s00894-009-0572-4"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1006/jmbi.1996.0477",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008061993"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-p",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009771619"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.540150207",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011046605"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.540150503",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012967303"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.21367",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014751155"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.21367",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014751155"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00894-007-0233-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021294303",
"https://doi.org/10.1007/s00894-007-0233-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00894-007-0233-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021294303",
"https://doi.org/10.1007/s00894-007-0233-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/bf01589116",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022481421",
"https://doi.org/10.1007/bf01589116"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/08927020600631270",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022539945"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1023/a:1011115820450",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024234487",
"https://doi.org/10.1023/a:1011115820450"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.20892",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024750196"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/00268977000101561",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031262511"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1006/jmbi.1996.0897",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031514441"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.20035",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033501081"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.540070216",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036800029"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja9621760",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043031881"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja9621760",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043031881"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/comjnl/7.4.308",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043067538"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.540141112",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046672215"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.1078",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047428156"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/jcc.10349",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049749105"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1214/aoms/1177729893",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049968279"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-b",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051500176"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.jmgm.2005.12.005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053541026"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ci0601214",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055402333"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ci0601214",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055402333"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ct049930p",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055423205"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ct049930p",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055423205"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00124a002",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055708364"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00205a001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055714115"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00205a002",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055714116"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00205a003",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055714117"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00214a001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055714735"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/ja00467a001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055734834"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jm020406h",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055947470"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/jm020406h",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1055947470"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1063/1.1756583",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1057815717"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/protein/7.3.385",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1059981031"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1017/cbo9781139167864",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1098662791"
],
"type": "CreativeWork"
}
],
"datePublished": "2012-02",
"datePublishedReg": "2012-02-01",
"description": "The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special \"closure\" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds.",
"genre": "research_article",
"id": "sg:pub.10.1007/s00894-011-1095-3",
"inLanguage": [
"en"
],
"isAccessibleForFree": false,
"isPartOf": [
{
"id": "sg:journal.1118122",
"issn": [
"1610-2940",
"0948-5023"
],
"name": "Journal of Molecular Modeling",
"type": "Periodical"
},
{
"issueNumber": "2",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "18"
}
],
"name": "Ab initio parameterization of YFF1, a universal force field for drug-design applications",
"pagination": "663-673",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"7414df33a8c98eb2bf314bf644e56ae92e30253c0148bb9e143e0f7dcf88adc6"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"21562826"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"9806569"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1007/s00894-011-1095-3"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1024365866"
]
}
],
"sameAs": [
"https://doi.org/10.1007/s00894-011-1095-3",
"https://app.dimensions.ai/details/publication/pub.1024365866"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T13:08",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8659_00000488.jsonl",
"type": "ScholarlyArticle",
"url": "http://link.springer.com/10.1007/s00894-011-1095-3"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s00894-011-1095-3'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s00894-011-1095-3'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00894-011-1095-3'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00894-011-1095-3'
This table displays all metadata directly associated to this object as RDF triples.
245 TRIPLES
21 PREDICATES
70 URIs
27 LITERALS
15 BLANK NODES