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Updated: Mar 31, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

ProTSAV: A protein tertiary structure analysis and validation server.

Ankita Singh¹, Rahul Kaushik², Avinash Mishra²

¹Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi, India; Department of Bioinformatics, Banasthali Vidyapith, Banasthali, 304022, India.

Biochimica Et Biophysica Acta

|October 20, 2015

Summary

This summary is machine-generated.

ProTSAV is a new server for assessing protein model structure quality. It provides a single score and ranking, proving robust and accurate for diverse protein structure datasets.

Keywords:

Protein structure quality assessment Structure evaluation Structure validation

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Area of Science:

Structural Biology
Computational Biology
Bioinformatics

Background:

Accurate quality assessment of predicted protein structures is crucial for downstream functional analysis.
Existing methods for protein model quality evaluation have limitations.

Purpose of the Study:

To develop and validate ProTSAV, a novel server for efficient and robust quality assessment of predicted protein model structures.
To provide users with a unified quality score and graphical representation for individual and multiple protein structure assessments.

Main Methods:

ProTSAV evaluates predicted protein model structures using data from popular online servers and standalone tools.
The server was validated on a large dataset (~64,446 structures) including experimental (RCSB) and predicted (CASP targets, decoy sets) protein structures.

Main Results:

ProTSAV achieved high accuracy: 100% specificity and 98% sensitivity on experimentally solved structures.
On predicted protein structures (CASP11 targets <2Å), ProTSAV demonstrated 88% specificity and 91% sensitivity.
The server integrates multiple assessment methods, overcoming limitations of single approaches.

Conclusions:

ProTSAV offers a robust and accurate solution for protein model structure quality assessment.
The server's integrated approach enhances reliability and aids in selecting high-quality protein models for further research.