Verification of protein structures: patterns of nonbonded atomic interactions

Protein Science : a Publication of the Protein Society
C Colovos, T O Yeates

Abstract

A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window.

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Citations

Nov 1, 1995·Journal of Molecular Recognition : JMR·N PattabiramanP J Fleming
Jan 16, 2002·Protein Science : a Publication of the Protein Society·Francisco MeloAndrej Sali
May 6, 1998·Protein Science : a Publication of the Protein Society·L J BeamerD Eisenberg
Jul 20, 2010·Cellular and Molecular Life Sciences : CMLS·Sergiy KostenkoUgo Moens
Apr 20, 2007·European Biophysics Journal : EBJ·Valentina ButtaniAba Losi
Jan 13, 2006·Journal of Molecular Modeling·Rong-Ren KuangDong-Zhi Wei
Aug 12, 2005·Journal of Molecular Modeling·Subramanian JyothiRajani R Joshi
May 4, 2005·Journal of Molecular Modeling·Santhanam Vijayasri, Shipra Agrawal
May 21, 2008·Journal of Molecular Modeling·Peter KyomuhendoArne O Smalås
Jul 16, 2008·Journal of Molecular Modeling·Minyong LiBinghe Wang
Feb 25, 2009·Journal of Molecular Modeling·Aina W RavnaSvein G Dahl
Aug 4, 2009·Journal of Molecular Modeling·Mahendra AwaleC Gopi Mohan
Feb 25, 2010·Journal of Molecular Modeling·Xiaojian WangQidong You
Aug 26, 2011·Journal of Molecular Modeling·Pawan Kumar RaghavGurudutta U Gangenahalli
May 16, 2013·Journal of Molecular Modeling·Chhavi DawarSudhir Kumar
Jul 3, 2013·Journal of Molecular Modeling·Anandan SwathiKrishnaswamy Gopalan Tirumurugaan
Oct 23, 2012·Functional & Integrative Genomics·Sarita PandeyL C Rai
Jul 25, 2007·Journal of Computer-aided Molecular Design·Luc RoumenJ J R Hermans
Jan 31, 2008·Journal of Computer-aided Molecular Design·P AparoyP Reddanna

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