PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-05-10 DOI:10.1093/nar/gkaf401

Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová

引用次数: 0

Abstract

The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has no login requirement.

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PDB电荷：PDB结构的量子力学部分原子电荷

蛋白质数据库（PDB）是最大的实验确定的蛋白质结构数据库，包含超过23万个实验确定的结构。蛋白质的化学反应性以电子密度分布为基础，通常用部分原子电荷来近似。然而，由于尺寸和高度可变性，目前还没有一种通用的和准确的工具来计算这些结构的部分原子电荷。出于这个原因，我们介绍了一个web应用程序PDBCharges：一个从PDB中快速计算蛋白质结构部分原子电荷的工具。利用最近的半经验量子力学方法GFN1-xTB计算电荷，该方法再现了PBE0/TZVP/CM5电荷。计算出的部分原子电荷可以以常见的数据格式下载或通过强大的Mol* Viewer在线可视化。PDBCharges应用程序可在https://pdbcharges.biodata.ceitec.cz免费获得，不需要登录。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.