Diverse Effects of Distance Cutoff and Residue Interval on the Performance of Distance-dependent Atom-pair Potential in Protein Structure Prediction

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2017 Dec 10

PMID 29221443

Citations 2

Authors

Yuangen Yao

Rong Gui

Quan Liu

Ming Yi

Haiyou Deng

Affiliations

Soon will be listed here.

Abstract

Background: As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model refinement, and model assessment. During the last two decades, great efforts have been made to improve the reference state of the potential, while other factors that also strongly affect the performance of the potential have been relatively less investigated.

Results: Based on different distance cutoffs (from 5 to 22 Å) and residue intervals (from 0 to 15) as well as six different reference states, we constructed a series of distance-dependent atom-pair potentials and tested them on several groups of structural decoy sets collected from diverse sources. A comprehensive investigation has been performed to clarify the effects of distance cutoff and residue interval on the potential's performance. Our results provide a new perspective as well as a practical guidance for optimizing distance-dependent statistical potentials.

Conclusions: The optimal distance cutoff and residue interval are highly related with the reference state that the potential is based on, the measurements of the potential's performance, and the decoy sets that the potential is applied to. The performance of distance-dependent statistical potential can be significantly improved when the best statistical parameters for the specific application environment are adopted.

Citing Articles

A simple neural network implementation of generalized solvation free energy for assessment of protein structural models.

Long S, Tian P RSC Adv. 2022; 9(62):36227-36233.

PMID: 35540566 PMC: 9074945. DOI: 10.1039/c9ra05168f.

ANDIS: an atomic angle- and distance-dependent statistical potential for protein structure quality assessment.

Yu Z, Yao Y, Deng H, Yi M BMC Bioinformatics. 2019; 20(1):299.

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