Stereochemical Assessment of (phi,psi) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps

Ravikumar, Ashraya and Ramakrishnan, Chandrasekharan and Srinivasan, Narayanaswamy (2019) Stereochemical Assessment of (phi,psi) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps. In: STRUCTURE, 27 (12). 1875+.

	PDF str_27-12_1875_2019.pdf - Published Version Restricted to Registered users only Download (2MB) | Request a copy
	Archive (ZIP) ScienceDirect_files_19Dec2019_11-40-36.764.zip - Published Supplemental Material Download (7MB)

Abstract

Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (phi,psi) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (phi,psi) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (phi,psi) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (phi,psi) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps.

Item Type:	Journal Article
Publication:	STRUCTURE
Publisher:	CELL PRESS
Additional Information:	Copyright of this article belongs to CELL PRESS
Keywords:	DISALLOWED CONFORMATIONS; ALLOWED CONFORMATIONS; STRUCTURE VALIDATION; HIDDEN STRAIN; POLYPEPTIDE; PEPTIDE; RESIDUES; QUALITY; PLOT
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	30 Dec 2019 09:05
Last Modified:	30 Dec 2019 09:05
URI:	http://eprints.iisc.ac.in/id/eprint/64191

Actions (login required)

View Item