UANanoDock: A Web-Based UnitedAtom Multiscale Nanodocking Tool for Predicting Protein Adsorption onto Nanoparticles.

IF 5.6 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2025-03-25 DOI:10.1021/acs.jcim.4c02292

Julia Subbotina, Panagiotis D Kolokathis, Andreas Tsoumanis, Nikolaos K Sidiropoulos, Ian Rouse, Iseult Lynch, Vladimir Lobaskin, Antreas Afantitis

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引用次数: 0

Abstract

UANanoDock is a web-based application with a graphical user interface designed for modeling protein-nanomaterial interactions, accessible via the Enalos Cloud Platform (https://www.enaloscloud.novamechanics.com/compsafenano/uananodock/). The application's foundation lies in the UnitedAtom multiscale model, previously reported for predicting the adsorption energies of biopolymers and small molecules onto nanoparticles (NPs). UANanoDock offers insights into optimal protein orientations when bound to spherical NP surfaces, considering factors such as material type, NP radius, surface potential, and amino acid (AA) ionization states at specific pH levels. The tool's computational time is determined solely by the protein's AA count, regardless of NP size. With its efficiency (e.g., approximately 60 s processing time for a 1331 AA protein) and versatility (accommodating any protein with a standard AA sequence in PDB format), UANanoDock serves as a prescreening tool for identifying proteins likely to adsorb onto NP surfaces. An illustration of UANanoDock's utility is provided, demonstrating its application in the rational design of immunoassays by determining the preferred orientation of the immunoglobulin G (IgG) antibody adsorbed on Ag NPs.

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来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.