Affiliation:
1. Institute of Informatics Federal University of Rio Grande do Sul Porto Alegre RS Brazil
2. Center for Biotechnology Federal University of Rio Grande do Sul Porto Alegre RS Brazil
3. National Institute of Forensic Science and Technology Federal University of Rio Grande do Sul Porto Alegre RS Brazil
Abstract
AbstractIncreasing the repertoire of available complementary tools to advance the knowledge of protein structures is fundamental for structural biology. The Neighbors Influence of Amino Acids and Secondary Structures (NIAS) is a server that analyzes a protein's conformational preferences of amino acids. NIAS is based on the Angle Probability List, representing the normalized frequency of empirical conformational preferences, such as torsion angles, of different amino acid pairs and their corresponding secondary structure information, as available in the Protein Data Bank. In this work, we announce the updated NIAS server with the data comprising all structures deposited until Sep 2022, 7 years after the initial release. Unlike the original publication, which accounted for only studies conducted with X‐ray crystallography, we added data from solid nuclear magnetic resonance (NMR), solution NMR, CullPDB, Electron Microscopy, and Electron Crystallography using multiple filtering parameters. We also provide examples of how NIAS can be applied as a complementary analysis tool for different structural biology works and what are its limitations.
Funder
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul
Subject
Computational Mathematics,General Chemistry