{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:19:59Z","timestamp":1674674399965},"reference-count":47,"publisher":"World Scientific Pub Co Pte Lt","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2007,6]]},"abstract":"<jats:p> In this study, we address the issue of performing meaningful pK<jats:sub>a<\/jats:sub> calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pK<jats:sub>a<\/jats:sub> values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pK<jats:sub>a<\/jats:sub> calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pK<jats:sub>a<\/jats:sub> values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pK<jats:sub>a<\/jats:sub> calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pK<jats:sub>a<\/jats:sub> fluctuations among the models or have pK<jats:sub>a<\/jats:sub> values shifted by several pH units with respect to the pK<jats:sub>a<\/jats:sub> calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pK<jats:sub>a<\/jats:sub> calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pK<jats:sub>a<\/jats:sub> values for highly conserved titratable residues within large sets of homologous proteins. <\/jats:p>","DOI":"10.1142\/s0219720007002709","type":"journal-article","created":{"date-parts":[[2007,8,9]],"date-time":"2007-08-09T20:32:00Z","timestamp":1186691520000},"page":"693-715","source":"Crossref","is-referenced-by-count":3,"title":["ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES"],"prefix":"10.1142","volume":"05","author":[{"given":"PETRAS","family":"KUNDROTAS","sequence":"first","affiliation":[{"name":"Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"PAULINA","family":"GEORGIEVA","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"ALEXANDRA","family":"SHOSHEVA","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"PETYA","family":"CHRISTOVA","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"EMIL","family":"ALEXOV","sequence":"additional","affiliation":[{"name":"Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1126\/science.7761829"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00514a028"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(98)80041-9"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1021\/bi00244a033"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1021\/bi052183d"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1021\/bi982700a"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20107"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560030206"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1021\/bi027202n"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.32.110601.141807"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1110\/ps.03114903"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.211436698"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720005000916"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20418"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1023\/A:1021220208562"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/12.8.657"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10265"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1110\/ps.0229903"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1002\/prot.1053"},{"key":"rf20","first-page":"2075","volume":"74","author":"Alexov E.","journal-title":"Biophys. 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