{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T06:23:48Z","timestamp":1783578228956,"version":"3.55.0"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"S1","license":[{"start":{"date-parts":[[2011,2,15]],"date-time":"2011-02-15T00:00:00Z","timestamp":1297728000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-s1-s34","type":"journal-article","created":{"date-parts":[[2011,2,18]],"date-time":"2011-02-18T20:09:53Z","timestamp":1298059793000},"source":"Crossref","is-referenced-by-count":50,"title":["Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories"],"prefix":"10.1186","volume":"12","author":[{"given":"Igor","family":"Chikalov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peggy","family":"Yao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail","family":"Moshkov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Claude","family":"Latombe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2011,2,15]]},"reference":[{"key":"4392_CR1","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1107\/97809553602060000711","volume":"F","author":"EN Baker","year":"2006","unstructured":"Baker EN: Hydrogen bonding in biological macromolecules. International Tables for Crystallography 2006, F: 546\u2013552. Chapter 22.2 Chapter 22.2 full_text","journal-title":"International Tables for Crystallography"},{"key":"4392_CR2","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/0959-440X(93)90205-Y","volume":"3","author":"AR Fersht","year":"1993","unstructured":"Fersht AR, Serrano L: Principles in protein stability derived from protein engineering experiments. Curr. Opin. Struct. Biol 1993, 3: 75\u201383. 10.1016\/0959-440X(93)90205-Y","journal-title":"Curr. Opin. Struct. Biol"},{"key":"4392_CR3","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1002\/prot.20826","volume":"63","author":"D Schell","year":"2006","unstructured":"Schell D, Tsai J, Scholtz JM, Pace CN: Hydrogen bonding increases packing density in the protein interior. Proteins 2006, 63: 278\u2013282. 10.1002\/prot.20826","journal-title":"Proteins"},{"key":"4392_CR4","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.abb.2007.02.020","volume":"461","author":"Z Bikadi","year":"2007","unstructured":"Bikadi Z, Demko L, Hazai E: Functional and structural characterization of a protein based on analysis of its hydrogen bonding network by hydrogen bonding plot. Arch Biochem Biophys 2007, 461: 225\u2013234. 10.1016\/j.abb.2007.02.020","journal-title":"Arch Biochem Biophys"},{"key":"4392_CR5","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1002\/pro.5560060622","volume":"6","author":"BI Dahiyat","year":"1997","unstructured":"Dahiyat BI, Gordon DB, Mayo SL: Automated design of the surface positions of protein helices. Protein Science 1997, 6: 1333\u20131337. 10.1002\/pro.5560060622","journal-title":"Protein Science"},{"key":"4392_CR6","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/294379a0","volume":"294","author":"M Levitt","year":"1981","unstructured":"Levitt M: Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin unhibitor protein. Nature 1981, 294: 379\u2013380. 10.1038\/294379a0","journal-title":"Nature"},{"key":"4392_CR7","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/S1093-3263(00)00122-4","volume":"19","author":"MF Thorpe","year":"2001","unstructured":"Thorpe MF, Lei M, Rader AJ, Jacobs DJ, Kuhn LA: Protein flexibility and dynamics using constraint theory. J. Mol. Graph. Model 2001, 19: 60\u201369. 10.1016\/S1093-3263(00)00122-4","journal-title":"J. Mol. Graph. Model"},{"key":"4392_CR8","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1006\/jmbi.1994.1334","volume":"238","author":"IK McDonald","year":"1994","unstructured":"McDonald IK, Thornton JM: Satisfying hydrogen bonding potential in proteins. J. Mol. Biol 1994, 238: 777\u2013793. 10.1006\/jmbi.1994.1334","journal-title":"J. Mol. Biol"},{"key":"4392_CR9","volume-title":"Classification and regression trees","author":"L Breiman","year":"1984","unstructured":"Breiman L, Friedman JH, Ilshen RA, Stone CJ: Classification and regression trees. CRC Press; 1984."},{"key":"4392_CR10","volume-title":"Comput. Biol. Chem","author":"H Joo","year":"2010","unstructured":"Joo H, Qu X, Swanson R, McCallum CM, Tsai J: Modeling the dependency of residue packing upon backbone conformation using molecular dynamics simulation. Comput. Biol. Chem 2010."},{"key":"4392_CR11","doi-asserted-by":"publisher","first-page":"1894","DOI":"10.1110\/ps.036624.108","volume":"17","author":"N Haspel","year":"2008","unstructured":"Haspel N, Ricklin D, Geisbrecht B, Lambris JD, Lydia EK: Electrostatic contributions drive the interaction between staphylococcus aureus protein Efb-C and its complement target C3d. Protein Sci 2008, 17: 1894\u20131906. 10.1110\/ps.036624.108","journal-title":"Protein Sci"},{"key":"4392_CR12","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/0010-4655(95)00049-L","volume":"91","author":"M Levitt","year":"1995","unstructured":"Levitt M, Hirshberg M, Sharon R, Daggett V: Potential Energy Function and Parameters for simulations of the Molecular Dynamics of Proteins and Nucleic Acids in Solution. Computer Physics Communications 1995, 91: 215\u2013231. 10.1016\/0010-4655(95)00049-L","journal-title":"Computer Physics Communications"},{"key":"4392_CR13","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1007\/s002140050460","volume":"101","author":"J Srinivasan","year":"1999","unstructured":"Srinivasan J, Trevathan M, Beroza P, Case D: Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc 1999, 101: 426\u2013434.","journal-title":"Theor. Chem. Acc"},{"key":"4392_CR14","volume-title":"Springer-Verlag","author":"GA Jeffrey","year":"1991","unstructured":"Jeffrey GA, Saenger W: Hydrogen bonding in biological structures. In Springer-Verlag. Germany; 1991."},{"key":"4392_CR15","first-page":"1048","volume":"4224","author":"E Tuv","year":"2006","unstructured":"Tuv E, Borisov A, Torkokola K: Best subset feature selection for massive mixed-type problems. IDEAL 2006, 4224: 1048\u20131056.","journal-title":"IDEAL"},{"key":"4392_CR16","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1214\/aos\/1013203451","volume":"29","author":"JH Friedman","year":"2000","unstructured":"Friedman JH: Greedy Function Approximation: A Gradient Boosting Machine. Annals of Statistics 2000, 29: 1189\u20131232. 10.1214\/aos\/1013203451","journal-title":"Annals of Statistics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S34.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-S1-S34\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S1-S34.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:28:09Z","timestamp":1548239289000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S1-S34"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,2,15]]},"references-count":16,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4392"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s1-s34","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,2,15]]},"article-number":"S34"}}