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It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "2015-1-28", "volume": "43", "issue": "Database issue", "section": "", "partNumber": "", "partTitle": "", "pages": "D298-D299", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res", "DOI": "10.1093/nar/gku1046", "citationKey": "", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383893/", "accessDate": "2017-10-28T09:55:03Z", "PMID": "", "PMCID": "", "ISSN": "0305-1048", "archive": "", "archiveLocation": "", "shortTitle": "REBASE—a database for DNA restriction and modification", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 25378308\nPMCID: PMC4383893", "tags": [], "collections": [ "EVMUF5XD" ], "relations": {}, "dateAdded": "2017-10-28T09:55:03Z", "dateModified": "2017-10-28T09:55:03Z" } }, { "key": "6RT3METG", "version": 1860, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/6RT3METG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/6RT3METG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Stone", "parsedDate": "1998", "numChildren": 2 }, "data": { "key": "6RT3METG", "version": 1860, "itemType": "book", "title": "An Efficient Library For Parallel Ray Tracing And Animation", "creators": [ { "creatorType": "author", "firstName": "John Edward", "lastName": "Stone" } ], "abstractNote": "A parallel ray tracing library is presented for rendering high detail images of three dimensional geometry and computational fields. The library has been developed for use on distributed memory and shared memory parallel computers and can also run on sequential computers. Parallelism is achieved through the use of message passing and threads. It is shown that the library achieves almost linear scalability when run on large distributed memory parallel computers as well as large shared memory parallel computers. Several applications of parallel rendering are explored including rendering of CAD models, animation, magnetic resonance imaging, and visualization of volumetric flow fields. Ray tracing offers many advantages over polygon rendering techniques, in its innate parallelism, and quality of output.", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "1998", "publisher": "University of Missouri - Rolla", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CiteSeer", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "V46JNTHT" ], "relations": {}, "dateAdded": "2017-06-27T08:53:12Z", "dateModified": "2017-06-27T08:57:16Z" } }, { "key": "U4T8XVBM", "version": 1859, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/U4T8XVBM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/U4T8XVBM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/6RT3METG", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "U4T8XVBM", "version": 1859, "parentItem": "6RT3METG", "itemType": "attachment", "linkMode": "imported_url", "title": "Citeseer - 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The method is based on local-spin-density functional theory, using nonlocal pseudopotentials and a plane-wave basis set. Evaluations of Hamiltonian matrix elements and the operations on the wave functions are performed using a dual-space representation. The method, which does not involve a supercell, affords accurate efficient simulations of neutral or charged finite systems which possess, or may develop, multipole moments. Since the ground-state electronic energy and the forces on the ions are calculated for each nuclear configuration during a dynammical simulation, a relatively large time step can be used to integrate the classical equations of motion of the nuclei (1–10 fs, depending on the characteristic frequencies of the ionic degrees of freedom). The method is demonstrated via a study of the energetics, structure, and dynamics of the water dimer, (H2O)2, yielding results in agreement with experimental data and other theoretical calculations. In addition to the properties of the ground state of the dimer, higher-energy transition structures involved in transformations between equivalent structures of the (H2O)2 molecule, were studied, and finite temperature simulations of the dynamics of such transformations are presented.", "publicationTitle": "Physical Review B", "publisher": "", "place": "", "date": "July 15, 1993", "volume": "48", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "2081-2097", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Phys. Rev. B", "DOI": "10.1103/PhysRevB.48.2081", "citationKey": "", "url": "http://link.aps.org/doi/10.1103/PhysRevB.48.2081", "accessDate": "2016-11-24T16:49:10Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Born-Oppenheimer molecular-dynamics simulations of finite systems", "language": "", "libraryCatalog": "APS", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "FAMTRZ2U" ], "relations": {}, "dateAdded": "2016-11-24T16:49:10Z", "dateModified": "2016-12-19T12:54:56Z" } }, { "key": "DNM4DI9M", "version": 1856, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/DNM4DI9M", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/DNM4DI9M", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Hohenberg and Kohn", "parsedDate": "1964", "numChildren": 0 }, "data": { "key": "DNM4DI9M", "version": 1856, "itemType": "journalArticle", "title": "Inhomogeneous Electron Gas", "creators": [ { "creatorType": "author", "firstName": "P.", "lastName": "Hohenberg" }, { "creatorType": "author", "firstName": "W.", "lastName": "Kohn" } ], "abstractNote": "", "publicationTitle": "Physical Review B", "publisher": "", "place": "", "date": "1964", "volume": "136", "issue": "3B", "section": "", "partNumber": "", "partTitle": "", "pages": "B864-B866", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Phys. Rev. B", "DOI": "10.1103/PhysRev.136.B864", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2469-9950", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "Web of Science", "callNumber": "", "rights": "", "extra": "WOS:A19641557C00018", "tags": [], "collections": [ "FAMTRZ2U" ], "relations": {}, "dateAdded": "2016-10-03T15:55:58Z", "dateModified": "2016-12-19T12:52:51Z" } }, { "key": "EJPR8KA7", "version": 1854, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/EJPR8KA7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/EJPR8KA7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/GK5VDNCE", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "EJPR8KA7", "version": 1854, "parentItem": "GK5VDNCE", "itemType": "attachment", "linkMode": "imported_url", "title": "PubMed Central Full Text PDF", "accessDate": "2016-12-13T18:35:12Z", "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299714/pdf/9649402.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Pace and Scholtz - 1998 - A helix propensity scale based on experimental stu.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2016-12-13T18:35:12Z", "dateModified": "2016-12-13T18:35:14Z" } }, { "key": "GK5VDNCE", "version": 1854, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/GK5VDNCE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/GK5VDNCE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Pace and Scholtz", "parsedDate": "1998-07", "numChildren": 2 }, "data": { "key": "GK5VDNCE", "version": 1854, "itemType": "journalArticle", "title": "A helix propensity scale based on experimental studies of peptides and proteins.", "creators": [ { "creatorType": "author", "firstName": "C N", "lastName": "Pace" }, { "creatorType": "author", "firstName": "J M", "lastName": "Scholtz" } ], "abstractNote": "The average globular protein contains 30% alpha-helix, the most common type of secondary structure. Some amino acids occur more frequently in alpha-helices than others; this tendency is known as helix propensity. Here we derive a helix propensity scale for solvent-exposed residues in the middle positions of alpha-helices. The scale is based on measurements of helix propensity in 11 systems, including both proteins and peptides. Alanine has the highest helix propensity, and, excluding proline, glycine has the lowest, approximately 1 kcal/mol less favorable than alanine. Based on our analysis, the helix propensities of the amino acids are as follows (kcal/mol): Ala = 0, Leu = 0.21, Arg = 0.21, Met = 0.24, Lys = 0.26, Gln = 0.39, Glu = 0.40, Ile = 0.41, Trp = 0.49, Ser = 0.50, Tyr = 0. 53, Phe = 0.54, Val = 0.61, His = 0.61, Asn = 0.65, Thr = 0.66, Cys = 0.68, Asp = 0.69, and Gly = 1.", "publicationTitle": "Biophysical Journal", "publisher": "", "place": "", "date": "1998-7", "volume": "75", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "422-427", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Biophys J", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299714/", "accessDate": "2016-12-13T18:35:12Z", "PMID": "", "PMCID": "", "ISSN": "0006-3495", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "PMID: 9649402\nPMCID: PMC1299714", "tags": [], "collections": [], "relations": {}, "dateAdded": "2016-12-13T18:35:12Z", "dateModified": "2016-12-13T18:35:12Z" } }, { "key": "4PVVAXD3", "version": 1854, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/4PVVAXD3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/4PVVAXD3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/GK5VDNCE", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } } }, "data": { "key": "4PVVAXD3", "version": 1854, "parentItem": "GK5VDNCE", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Central Link", "accessDate": "2016-12-13T18:35:12Z", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299714/", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-12-13T18:35:12Z", "dateModified": "2016-12-13T18:35:12Z" } }, { "key": "R8PMPDP8", "version": 1853, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/R8PMPDP8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/R8PMPDP8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Szczepanowski et al.", "parsedDate": "2007-12-12", "numChildren": 2 }, "data": { "key": "R8PMPDP8", "version": 1853, "itemType": "journalArticle", "title": "A direct crystallographic demonstration that Type II restriction endonuclease PspGI flips nucleotides", "creators": [ { "creatorType": "author", "firstName": "R. H.", "lastName": "Szczepanowski" }, { "creatorType": "author", "firstName": "M.", "lastName": "Carpenter" }, { "creatorType": "author", "firstName": "H.", "lastName": "Czapinska" }, { "creatorType": "author", "firstName": "G.", "lastName": "Tamulaitis" }, { "creatorType": "author", "firstName": "V.", "lastName": "Siksnys" }, { "creatorType": "author", "firstName": "A.", "lastName": "Bhagwat" }, { "creatorType": "author", "firstName": "M.", "lastName": "Bochtler" } ], "abstractNote": "", "publicationTitle": "To be Published", "publisher": "", "place": "", "date": "2007-12-12", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1-2", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "To be Published", "DOI": "", "citationKey": "", "url": "http://www.pdb.org/pdb/explore/explore.do?structureId=3bm3", "accessDate": "2014-05-21T16:46:05Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Protein Data Bank", "callNumber": "", "rights": "", "extra": "PMID: null", "tags": [], "collections": [ "EVMUF5XD" ], "relations": {}, "dateAdded": "2014-05-21T16:46:05Z", "dateModified": "2016-12-13T18:33:21Z" } }, { "key": "MMM5DDNU", "version": 1851, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/MMM5DDNU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/MMM5DDNU", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/63VRRTS5", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } } }, "data": { "key": "MMM5DDNU", "version": 1851, "parentItem": "63VRRTS5", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2016-12-13T16:05:28Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/20301239", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-12-13T16:05:28Z", "dateModified": "2016-12-13T16:05:28Z" } }, { "key": "63VRRTS5", "version": 1851, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/63VRRTS5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/63VRRTS5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Varki et al.", "parsedDate": "2009", "numChildren": 1 }, "data": { "key": "63VRRTS5", "version": 1851, "itemType": "book", "title": "Essentials of Glycobiology", "creators": [ { "creatorType": "editor", "firstName": "Ajit", "lastName": "Varki" }, { "creatorType": "editor", "firstName": "Richard D.", "lastName": "Cummings" }, { "creatorType": "editor", "firstName": "Jeffrey D.", "lastName": "Esko" }, { "creatorType": "editor", "firstName": "Hudson H.", "lastName": "Freeze" }, { "creatorType": "editor", "firstName": "Pamela", "lastName": "Stanley" }, { "creatorType": "editor", "firstName": "Carolyn R.", "lastName": "Bertozzi" }, { "creatorType": "editor", "firstName": "Gerald W.", "lastName": "Hart" }, { "creatorType": "editor", "firstName": "Marilynn E.", "lastName": "Etzler" } ], "abstractNote": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "2nd", "date": "2009", "publisher": "Cold Spring Harbor Laboratory Press", "place": "Cold Spring Harbor (NY)", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "978-0-87969-770-9", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/books/NBK1908/", "accessDate": "2016-12-13T16:05:28Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "NBK1908", "rights": "", "extra": "PMID: 20301239", "tags": [], "collections": [ "IWHXQW34" ], "relations": {}, "dateAdded": "2016-12-13T16:05:28Z", "dateModified": "2016-12-13T16:05:28Z" } }, { "key": "473IHT7G", "version": 1850, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/473IHT7G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/473IHT7G", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/VPKVXNQA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "473IHT7G", "version": 1850, "parentItem": "VPKVXNQA", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2016-12-08T14:07:15Z", "url": "http://link.springer.com/content/pdf/10.1007%2Fs00214-002-0413-3.pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Amara and Field - 2003 - Evaluation of an ab initio quantum mechanicalmole.pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2016-12-08T14:07:15Z", "dateModified": "2016-12-08T14:07:19Z" } }, { "key": "VPKVXNQA", "version": 1850, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/VPKVXNQA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/VPKVXNQA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Amara and Field", "parsedDate": "2003-02-01", "numChildren": 2 }, "data": { "key": "VPKVXNQA", "version": 1850, "itemType": "journalArticle", "title": "Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method", "creators": [ { "creatorType": "author", "firstName": "Patricia", "lastName": "Amara" }, { "creatorType": "author", "firstName": "Martin J.", "lastName": "Field" } ], "abstractNote": ". Hybrid potentials have become a common tool in the study of many condensed-phase processes and are the subject of much active research. An important aspect of the formulation of a hybrid potential concerns how to handle covalent bonds between atoms that are described with different potentials and, most notably, those at the interface of the quantum mechanical (QM) and molecular mechanical (MM) regions. Several methods have been proposed to deal with this problem, ranging from the simple link-atom method to more sophisticated hybrid-orbital techniques. Although it has been heavily criticized, the link-atom method has probably been the most widely used in applications, especially with hybrid potentials that use semiempirical QM methods. Our aim in this paper has been to evaluate the link-atom method for ab initio QM/MM hybrid potentials and to compare the results it gives with those of previously published studies. Given its simplicity and robustness, we find that the link-atom method can produce results of comparable accuracy to other methods as long as the charge distribution on the MM atoms at the interface is treated appropriately.", "publicationTitle": "Theoretical Chemistry Accounts", "publisher": "", "place": "", "date": "2003/02/01", "volume": "109", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "43-52", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Theor Chem Acc", "DOI": "10.1007/s00214-002-0413-3", "citationKey": "", "url": "http://link.springer.com/article/10.1007/s00214-002-0413-3", "accessDate": "2016-12-08T14:07:15Z", "PMID": "", "PMCID": "", "ISSN": "1432-881X, 1432-2234", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "link.springer.com", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "UWTSCVAV" ], "relations": {}, "dateAdded": "2016-12-08T14:07:15Z", "dateModified": "2016-12-08T14:07:15Z" } }, { "key": "MPQJ3QA5", "version": 1850, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/MPQJ3QA5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/MPQJ3QA5", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/VPKVXNQA", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } } }, "data": { "key": "MPQJ3QA5", "version": 1850, "parentItem": "VPKVXNQA", "itemType": "attachment", "linkMode": "imported_url", "title": "Snapshot", "accessDate": "2016-12-08T14:07:15Z", "url": "http://link.springer.com/article/10.1007%2Fs00214-002-0413-3", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "10.html", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2016-12-08T14:07:15Z", "dateModified": "2016-12-08T14:07:15Z" } }, { "key": "GX2NB9U7", "version": 1849, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/GX2NB9U7", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/GX2NB9U7", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/M4AHZFVX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } } }, "data": { "key": "GX2NB9U7", "version": 1849, "parentItem": "M4AHZFVX", "itemType": "attachment", "linkMode": "imported_url", "title": "ACS Full Text Snapshot", "accessDate": "2016-12-08T14:05:47Z", "url": "http://pubs.acs.org/doi/full/10.1021/jp9536514", "note": "", "contentType": "text/html", "charset": "utf-8", "filename": "jp9536514.html", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2016-12-08T14:05:47Z", "dateModified": "2016-12-08T14:05:47Z" } }, { "key": "APUAHRGW", "version": 1849, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/APUAHRGW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/APUAHRGW", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/6195/items/M4AHZFVX", "type": "application/json" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "APUAHRGW", "version": 1849, "parentItem": "M4AHZFVX", "itemType": "attachment", "linkMode": "imported_url", "title": "ACS Full Text PDF w/ Links", "accessDate": "2016-12-08T14:05:39Z", "url": "http://pubs.acs.org/doi/pdfplus/10.1021/jp9536514", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Bakowies and Thiel - 1996 - Hybrid Models for Combined Quantum Mechanical and .pdf", "md5": null, "mtime": null, "tags": [], "relations": {}, "dateAdded": "2016-12-08T14:05:39Z", "dateModified": "2016-12-08T14:05:41Z" } }, { "key": "M4AHZFVX", "version": 1849, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/M4AHZFVX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/M4AHZFVX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Bakowies and Thiel", "parsedDate": "1996-01-01", "numChildren": 2 }, "data": { "key": "M4AHZFVX", "version": 1849, "itemType": "journalArticle", "title": "Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches", "creators": [ { "creatorType": "author", "firstName": "Dirk", "lastName": "Bakowies" }, { "creatorType": "author", "firstName": "Walter", "lastName": "Thiel" } ], "abstractNote": "A hierarchy of three models for combined quantum mechanical (QM) and molecular mechanical (MM) approaches is presented. They simplify the QM description of large molecules by reducing it to the electronically important fragment which interacts with the molecular mechanically treated remainder of the molecule. In the simplest model A, the QM fragments are only mechanically embedded in their MM environment. The more refined models B and C include a quantum mechanical treatment of electrostatic interactions between the fragments and a semiclassical description of polarization. The implementation of models A-C for MNDO type wavefunctions and the MM3 force field is outlined. Selected applications in organic chemistry are discussed, addressing the ability of the proposed models to reproduce substituent effects (MM) on chemical structure and reactivity (QM). These applications include protonations, deprotonations, hydride transfer reactions, nucleophilic additions, and nucleophilic ring cleavage reactions.", "publicationTitle": "The Journal of Physical Chemistry", "publisher": "", "place": "", "date": "January 1, 1996", "volume": "100", "issue": "25", "section": "", "partNumber": "", "partTitle": "", "pages": "10580-10594", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Phys. Chem.", "DOI": "10.1021/jp9536514", "citationKey": "", "url": "http://dx.doi.org/10.1021/jp9536514", "accessDate": "2016-12-08T14:05:39Z", "PMID": "", "PMCID": "", "ISSN": "0022-3654", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ACS Publications", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "UWTSCVAV" ], "relations": {}, "dateAdded": "2016-12-08T14:05:39Z", "dateModified": "2016-12-08T14:05:39Z" } }, { "key": "SKU44IJC", "version": 1848, "library": { "type": "group", "id": 6195, "name": "Stepan Jakub", "links": { "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/6195/items/SKU44IJC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/stepan_jakub/items/SKU44IJC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 52363, "username": "Jakub Stepan", "name": "Jakub Stepan", "links": { "alternate": { "href": "https://www.zotero.org/jakub_stepan", "type": "text/html" } } }, "creatorSummary": "Eurenius et al.", "parsedDate": "1996-12-10", "numChildren": 0 }, "data": { "key": "SKU44IJC", "version": 1848, "itemType": "journalArticle", "title": "Enzyme mechanisms with hybrid quantum and molecular mechanical potentials .1. Theoretical considerations", "creators": [ { "creatorType": "author", "firstName": "K. P.", "lastName": "Eurenius" }, { "creatorType": "author", "firstName": "D. C.", "lastName": "Chatfield" }, { "creatorType": "author", "firstName": "B. R.", "lastName": "Brooks" }, { "creatorType": "author", "firstName": "M.", "lastName": "Hodoscek" } ], "abstractNote": "The application of hybrid quantum mechanical and molecular mechanical (QM/MM) potentials to the study of chemical reactions in enzymes is outlined. The discussion is general and addresses the difficulties encountered in an enzyme QM/MM study. First, general criteria for determining whether a particular enzyme is an appropriate candidate for a QM/MM approach are outlined. Methods for obtaining starting structures are detailed. The importance of choosing appropriate levels of ab initio or semiempirical theory is emphasized. Approaches for interfacing the QM and MM regions are briefly discussed, with greater detail given to describing our CHARMM-GAMESS interface. Techniques for partitioning the system into QM and MM regions are explored. Link atom placement, as distant from reacting atoms as possible within the confines of computational efficiency, is examined in some detail. Methods for determining reaction paths are also discussed. (C) 1996 John Wiley & Sons, Inc.", "publicationTitle": "International Journal of Quantum Chemistry", "publisher": "", "place": "", "date": "DEC 10 1996", "volume": "60", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1189-1200", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Int. J. 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