# DBT JRF 2020 — Question 109

Exam: DBT JRF 2020 · Section: B · Topic: Bioinformatics · Difficulty: Hard

## Question

Accuracy of Protein Structure Prediction can be assessed using tools like

## Options

- **A.** BLAST
- **B.** PHENIX
- **C.** COOT
- **D.** WHATIF

## Answer

Option D

## Explanation

WHATIF (now part of the WHATCHECK server) is a protein structure verification and analysis program developed by Gerrit Vriend. It assesses structural quality by checking: backbone geometry (bond lengths, angles, Ramachandran plot), side-chain rotamers, packing quality (bumps, contacts), polar hydrogen positions, and model completeness. It generates a PDBREPORT for any deposited or predicted structure. BLAST (Basic Local Alignment Search Tool): sequence similarity searching tool — not for structure quality. PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography): software suite for X-ray crystal structure DETERMINATION from diffraction data. COOT (Crystallographic Object-Oriented Toolkit): interactive molecular graphics for model building and fitting electron density maps. WHATIF is specifically for structure ASSESSMENT/VERIFICATION — used as a final check before structure deposition.

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