ArticleNucleic acids research2013
The FunFOLD2 server for the prediction of protein-ligand interactions.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed.
- Solanum bulbocastanum nucleotide-binding leucine-rich repeat receptor evolution reveals functional variants and critical residues in Rpi-blb1/RB.Journal of integrative plant biology · 2025Article
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- Genetic analysis of PALB2 gene WD40 domain in canine mammary tumour patients.Veterinary medicine and science · 2024Article
- Structural Insights into theInternational journal of molecular sciences · 2023Article
- Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers.Nucleic acids research · 2023Article
- In Silico Examination of Single Nucleotide Missense Mutations inInternational journal of molecular sciences · 2023Article
- In Silico Structural Analysis of Serine CarboxypeptidaseInternational journal of molecular sciences · 2022Article
- A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level.BioMed research international · 2022Review
- Article
- Article
- Structure-Function Relationship Study of a Secretory Amoebic Phosphatase: A Computational-Experimental Approach.International journal of molecular sciences · 2021Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3.Methods in molecular biology (Clifton, N.J.) · 2021Article
- "The Good, the Bad and the Double-Sword" Effects of Microplastics and Their Organic Additives in Marine Bacteria.Frontiers in microbiology · 2020Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- IntFOLD: an integrated web resource for high performance protein structure and function prediction.Nucleic acids research · 2019Article
- Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene,3 Biotech · 2018Article
- COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking.Nucleic acids research · 2018Article
- A web server for analysis, comparison and prediction of protein ligand binding sites.Biology direct · 2016Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.International journal of molecular sciences · 2015Review
- Modeling enzyme-ligand binding in drug discovery.Journal of cheminformatics · 2015Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The FunFOLD2 server is a new independent server that integrates our novel protein-ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein-ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.
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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.