{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T00:50:40Z","timestamp":1680655840119},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2012,4,1]],"date-time":"2012-04-01T00:00:00Z","timestamp":1333238400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2012,4]]},"DOI":"10.1007\/s10822-012-9564-z","type":"journal-article","created":{"date-parts":[[2012,4,3]],"date-time":"2012-04-03T09:18:45Z","timestamp":1333444725000},"page":"387-396","source":"Crossref","is-referenced-by-count":1,"title":["A collaborative environment for developing and validating predictive tools for protein biophysical characteristics"],"prefix":"10.1007","volume":"26","author":[{"given":"Michael A.","family":"Johnston","sequence":"first","affiliation":[]},{"given":"Damien","family":"Farrell","sequence":"additional","affiliation":[]},{"given":"Jens Erik","family":"Nielsen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,4,4]]},"reference":[{"issue":"12","key":"9564_CR1","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/nsb1203-980","volume":"10","author":"H Berman","year":"2003","unstructured":"Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10(12):980","journal-title":"Nat Struct Biol"},{"issue":"Database issue","key":"9564_CR2","doi-asserted-by":"crossref","first-page":"D129","DOI":"10.1093\/nar\/gkh028","volume":"32","author":"CT Porter","year":"2004","unstructured":"Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32(Database issue):D129\u2013D133","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"9564_CR3","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gkj103","volume":"34","author":"MDS Kumar","year":"2006","unstructured":"Kumar MDS, Bava KA, Gromiha MM, Prabakaran P, Kitajima K, Uedaira H, Sarai A (2006) ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res 34(Database issue):D204\u2013D206","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"9564_CR4","doi-asserted-by":"crossref","first-page":"D511","DOI":"10.1093\/nar\/gkl972","volume":"35","author":"J Barthelmes","year":"2007","unstructured":"Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D (2007) BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res 35(Database issue):D511\u2013D514","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"9564_CR5","doi-asserted-by":"crossref","first-page":"D199","DOI":"10.1093\/nar\/gkj035","volume":"34","author":"CP Toseland","year":"2006","unstructured":"Toseland CP, McSparron H, Davies MN, Flower DR (2006) PPD v1.0\u2013an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res 34(Database issue):D199\u2013D203","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"9564_CR6","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1002\/prot.22611","volume":"78","author":"D Farrell","year":"2010","unstructured":"Farrell D, Miranda ES, Webb H, Georgi N, Crowley PB, McIntosh LP, Nielsen JE (2010) Titration_DB: storage and analysis of NMR-monitored protein pH titration curves. Proteins 78(4):843\u2013857","journal-title":"Proteins"},{"issue":"Database issue","key":"9564_CR7","doi-asserted-by":"crossref","first-page":"D522","DOI":"10.1093\/nar\/gkj039","volume":"34","author":"P Block","year":"2006","unstructured":"Block P, Sotriffer CA, Dramburg I, Klebe G (2006) AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. Nucleic Acids Res 34(Database issue):D522\u2013D526","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"9564_CR8","doi-asserted-by":"crossref","first-page":"D198","DOI":"10.1093\/nar\/gkl999","volume":"35","author":"T Liu","year":"2007","unstructured":"Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35(Database issue):D198\u2013D201","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"9564_CR9","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","volume":"48","author":"R Wang","year":"2005","unstructured":"Wang R, Fang X, Lu Y, Yang C-Y, Wang S (2005) The PDBbind database: methodologies and updates. J Med Chem 48(12):4111\u20134119","journal-title":"J Med Chem"},{"issue":"Database issue","key":"9564_CR10","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","volume":"37","author":"LJ Jensen","year":"2009","unstructured":"Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C (2009) STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37(Database issue):D412\u2013D416","journal-title":"Nucleic Acids Res"},{"key":"9564_CR11","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/S0076-6879(04)83004-0","volume":"383","author":"CA Rohl","year":"2004","unstructured":"Rohl CA, Strauss CEM, Misura KMS, Baker D (2004) Protein Structure Prediction Using Rosetta. Methods Enzymol 383:66\u201393","journal-title":"Methods Enzymol"},{"key":"9564_CR12","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2105-9-40","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"9564_CR13","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1002\/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.0.CO;2-H","volume":"39","author":"YY Sham","year":"2000","unstructured":"Sham YY, Chu ZT, Tao H, Warshel A (2000) Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD\/S-LRA calculations of ligands binding to an HIV protease. Proteins 39(4):393\u2013407","journal-title":"Proteins"},{"issue":"12","key":"9564_CR14","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1021\/jm0203783","volume":"46","author":"R Wang","year":"2003","unstructured":"Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46(12):2287\u20132303","journal-title":"J Med Chem"},{"issue":"4","key":"9564_CR15","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/prot.20660","volume":"61","author":"H Li","year":"2005","unstructured":"Li H, Robertson AD, Jensen JH (2005) Very fast empirical prediction and rationalization of protein pKa values. Proteins 61(4):704\u2013721","journal-title":"Proteins"},{"issue":"Web Server issu","key":"9564_CR16","doi-asserted-by":"crossref","first-page":"W48","DOI":"10.1093\/nar\/gkl192","volume":"34","author":"BM Tynan-Connolly","year":"2006","unstructured":"Tynan-Connolly BM, Nielsen JE (2006) pKD: re-designing protein pKa values. Nucleic Acids Res 34(Web Server issue):W48\u2013W51","journal-title":"Nucleic Acids Res"},{"issue":"5723","key":"9564_CR17","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1126\/science.1107387","volume":"308","author":"A Korkegian","year":"2005","unstructured":"Korkegian A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme. Science 308(5723):857\u2013860","journal-title":"Science"},{"issue":"9","key":"9564_CR18","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1093\/protein\/gzp030","volume":"22","author":"V Potapov","year":"2009","unstructured":"Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 22(9):553\u2013560","journal-title":"Protein Eng Des Sel"},{"issue":"10","key":"9564_CR19","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1038\/nbt1018","volume":"22","author":"P Aloy","year":"2004","unstructured":"Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22(10):1317\u20131321","journal-title":"Nat Biotechnol"},{"issue":"5666","key":"9564_CR20","doi-asserted-by":"crossref","first-page":"2026","DOI":"10.1126\/science.1092645","volume":"303","author":"P Aloy","year":"2004","unstructured":"Aloy P, B\u00f6ttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin A-C, Bork P, Superti-Furga G, Serrano L, Russell RB (2004) Structure-based assembly of protein complexes in yeast. Science 303(5666):2026\u20132029","journal-title":"Science"},{"issue":"5","key":"9564_CR21","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1021\/cr040427e","volume":"106","author":"MHM Olsson","year":"2006","unstructured":"Olsson MHM, Parson WW, Warshel A (2006) Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis. Chem Rev 106(5):1737\u20131756","journal-title":"Chem Rev"},{"issue":"10","key":"9564_CR22","doi-asserted-by":"crossref","first-page":"6544","DOI":"10.1073\/pnas.082657099","volume":"99","author":"T Simonson","year":"2002","unstructured":"Simonson T (2002) Gaussian fluctuations and linear response in an electron transfer protein. Proc Natl Acad Sci U S A, 99(10):6544\u20136549","journal-title":"Proc Natl Acad Sci U S A,"},{"key":"9564_CR23","doi-asserted-by":"crossref","unstructured":"Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE (2011) On the development of protein pKa calculation algorithms. Proteins. doi: 10.1002\/prot.23091","DOI":"10.1002\/prot.23091"},{"issue":"suppl 2","key":"9564_CR24","doi-asserted-by":"crossref","first-page":"W1","DOI":"10.1093\/nar\/gkq562","volume":"38","author":"G Benson","year":"2010","unstructured":"Benson G (2010) Editorial. Nucleic Acids Res 38(suppl 2):W1\u2013W2","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"9564_CR25","doi-asserted-by":"crossref","first-page":"e186","DOI":"10.1093\/nar\/gkq726","volume":"38","author":"D Farrell","year":"2010","unstructured":"Farrell D, O\u2019Meara F, Johnston M, Bradley J, S\u00f8ndergaard CR, Georgi N, Webb H, Tynan-Connolly BM, Bjarnadottir U, Carstensen T, Nielsen JE (2010) Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. Nucleic Acids Res 38(20):e186","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"9564_CR26","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1002\/prot.22870","volume":"79","author":"MA Johnston","year":"2011","unstructured":"Johnston MA, S\u00f8ndergaard CR, Nielsen JE (2011) Integrated prediction of the effect of mutations on multiple protein characteristics. Proteins 79(1):165\u2013178","journal-title":"Proteins"},{"issue":"2","key":"9564_CR27","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1110\/ps.062538707","volume":"16","author":"BM Tynan-Connolly","year":"2007","unstructured":"Tynan-Connolly BM, Nielsen JE (2007) Redesigning protein pKa values. Protein Sci 16(2):239\u2013249","journal-title":"Protein Sci"},{"issue":"Web Server issu","key":"9564_CR28","doi-asserted-by":"crossref","first-page":"W522","DOI":"10.1093\/nar\/gkm276","volume":"35","author":"TJ Dolinsky","year":"2007","unstructured":"Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35(Web Server issue):W522\u2013W525","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"9564_CR29","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0022-2836(02)00442-4","volume":"320","author":"G Guerois","year":"2002","unstructured":"Guerois G, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320(2):369\u2013387","journal-title":"J Mol Biol"},{"key":"9564_CR30","unstructured":"Bode B, Halstead DM, Kendall R, Lei Z, Jackson D (2000) The portable batch scheduler and the Maui scheduler on Linux clusters. In: ALS\u201900: Proceedings of the 4th Annual Linux Showcase & Conference. Berkeley, CA, USA: USENIX Association, pp 27\u201327"},{"key":"9564_CR31","doi-asserted-by":"crossref","unstructured":"Johnston MA, Nielsen JE (2011) Constructing and evaluating predictive models for protein biophysical characteristics. Ann Rep Comput Chem 7:101\u2013122. doi: 10.1016\/B978-0-444-53835-2.00012-2","DOI":"10.1016\/B978-0-444-53835-2.00012-2"},{"issue":"3","key":"9564_CR32","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/0022-2836(92)90562-X","volume":"224","author":"L Serrano","year":"1992","unstructured":"Serrano L, Kellis JT Jr, Cann P, Matouschek A, Fersht AR (1992) The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol 224(3):783\u2013804","journal-title":"J Mol Biol"},{"issue":"2","key":"9564_CR33","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1016\/0022-2836(92)90906-Z","volume":"227","author":"L Serrano","year":"1992","unstructured":"Serrano L, Sancho J, Hirshberg M, Fersht AR (1992) Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces. J Mol Biol 227(2):544\u2013559","journal-title":"J Mol Biol"},{"issue":"2","key":"9564_CR34","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1016\/0022-2836(92)90907-2","volume":"227","author":"A Horovitz","year":"1992","unstructured":"Horovitz A, Matthews JM, Fersht AR (1992) Alpha-helix stability in proteins. II. Factors that influence stability at an internal position. J Mol Biol 227(2):560\u2013568","journal-title":"J Mol Biol"},{"issue":"3","key":"9564_CR35","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48(3):443\u2013453","journal-title":"J Mol Biol"},{"key":"9564_CR36","doi-asserted-by":"crossref","unstructured":"Farrell D, Webb H, Johnston MA, Poulsen TA, Christensen LB, Borchert TV, Nielsen JE (2012) Towards fast determination of protein stability maps: experimental and theoretical analysis of mutants of a Nocardiopsis prasina serine protease. Biochemistry, Accepted for publication.","DOI":"10.1021\/bi201926f"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-012-9564-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10822-012-9564-z\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-012-9564-z","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,26]],"date-time":"2019-06-26T16:20:02Z","timestamp":1561566002000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10822-012-9564-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,4]]},"references-count":36,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2012,4]]}},"alternative-id":["9564"],"URL":"https:\/\/doi.org\/10.1007\/s10822-012-9564-z","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,4]]}}}