caa a22 4500 605510776 CHVBK 20210128100647.0 cr unu---uuuuu 210128e20150101xx s 000 0 eng 10.1007/s00894-014-2520-1 doi (NATIONALLICENCE)springer-10.1007/s00894-014-2520-1 An approach to creating a more realistic working model from a protein data bank entry [Elektronische Daten] [Christopher Brandon, Benjamin Martin, Kelly McGee, James Stewart, Sonja Braun-Sand] An accurate model of three-dimensional protein structure is important in a variety of fields such as structure-based drug design and mechanistic studies of enzymatic reactions. While the entries in the Protein Data Bank ( http://www.pdb.org ) provide valuable information about protein structures, a small fraction of the PDB structures were found to contain anomalies not reported in the PDB file. The semiempirical PM7 method in MOPAC2012 was used for identifying anomalously short hydrogen bonds, C-H⋯O/C-H⋯N interactions, non-bonding close contacts, and unrealistic covalent bond lengths in recently published Protein Data Bank files. It was also used to generate new structures with these faults removed. When the semiempirical models were compared to those of PDB_REDO ( http://www.cmbi.ru.nl/pdb_redo/ ), the clashscores, as defined by MolProbity ( http://molprobity.biochem.duke.edu/ ), were better in about 50% of the structures. The semiempirical models also had a lower root-mean-square-deviation value in nearly all cases than those from PDB_REDO, indicative of a better conservation of the tertiary structure. Finally, the semiempirical models were found to have lower clashscores than the initial PDB file in all but one case. Because this approach maintains as much of the original tertiary structure as possible while improving anomalous interactions, it should be useful to theoreticians, experimentalists, and crystallographers investigating the structure and function of proteins. Springer-Verlag Berlin Heidelberg, 2015 Semiempirical methods nationallicence PM7 nationallicence Protein data bank nationallicence Geometric anomalies nationallicence Brandon Christopher Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut Martin Benjamin Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut McGee Kelly Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut Stewart James Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut Braun-Sand Sonja Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/1(2015-01-01), 1-11 1610-2940 21:1<1 2015 21 894 https://doi.org/10.1007/s00894-014-2520-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-014-2520-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Brandon Christopher Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut NATIONALLICENCE 700 1- Martin Benjamin Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut NATIONALLICENCE 700 1- McGee Kelly Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut NATIONALLICENCE 700 1- Stewart James Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut NATIONALLICENCE 700 1- Braun-Sand Sonja Department of Chemistry and Biochemistry, University of Colorado, Colorado Springs, 80918, Colorado Springs, CO, USA aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/1(2015-01-01), 1-11 1610-2940 21:1<1 2015 21 894