ArticleNucleic acids research2025
ProteinsPlus: a publicly available resource for protein structure mining.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- PARP3 Promotes SARS-CoV-2 Replication via Interaction with the Viral Nucleocapsid Protein.The Kobe journal of medical sciences · 2026Article
- Computationally Generated Plant-Derived Berberine-Based Hybrid Compounds as Potential Dual Binders toInternational journal of molecular sciences · 2026Article
- Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning.Biomacromolecules · 2026Review
- Candimine as a natural scaffold for targeting squalene synthetase in Trypanosoma cruzi: insights from computational studies.Molecular diversity · 2026Article
- Machine learning-assisted screening of natural product database for the identification of novel chalcone-based derivative as a potent DHODH inhibitor in cancer therapy.Discover oncology · 2026Article
- Structural basis for inhibition of TcrXyn10A xylanase by nonspecific xylose binding at subsite - 2.Scientific reports · 2026Article
- Leveraging the antibacterial and antibiofilm activities of Cymbopogon flexuosus essential oil against multidrug-resistant bacteria recovered from avian colibacillosis and bovine mastitis: in vitro and molecular docking insights.Veterinary research communications · 2026Article
- Discovery of regulatory complexes in Arabidopsis via protein-metabolite mapping during Pseudomonas infection.Plant physiology · 2026Article
- Long-term artificial sweetener exposure increases the risk of atherosclerosis.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- QuantumPDB: A Workflow for High-Throughput Quantum Cluster Model Generation from Protein Structures.Journal of chemical information and modeling · 2026Article
- More than an attachment module: covalent inhibitor warheads influence BTK dynamics and function.bioRxiv : the preprint server for biology · 2026Article
- Gaining insights into MmpL3: combining structural and computational approaches to unlock transport and inhibitor-binding mechanisms.Acta crystallographica. Section D, Structural biology · 2026Article
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Antinociceptive Effect of Cinnamaldehyde in Male Mice: Investigation of the Mechanisms of Action Through In Silico and In Vivo Approaches.Chemistry & biodiversity · 2026Article
- Machine learning-driving optimization and spatial assembly of a cell-free system for high-yield liquiritigenin production.Advanced biotechnology · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The openly accessible ProteinsPlus web server at https://proteins.plus is a unique resource enabling protein structure mining and modeling, focussing on protein-ligand interactions. Since its launch in 2017, the number of tools is steadily increasing. Currently, the server comprises six methods for protein structure analysis, four tools for mining the Protein Data Bank (PDB), and five prediction approaches regarding protein-ligand complex modeling. Users can use experimental structures from the PDB or computationally predicted structures from the AlphaFold Protein Structure Database as starting points. Alternatively, they can upload individual structure files. Recent updates include novel methods for detecting binding sites and predicting solvent channels in crystallographic structures, as well as updates of tools for protein-ligand interaction depiction in 2D and binding site mining. Given these updates, we present a real-life application scenario that underpins the novelties and applicability of the web server's tools for modern structure-based design projects. It also highlights the next steps for the web server, which will be redesigned using a different technology stack to improve the inter-usability of the tools, ease maintainability, and make it future-proof.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.