ReviewInternational journal of molecular sciences2015
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.
Review in International journal of molecular sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.Journal of chemical information and modeling · 2026Article
- Hybrid protein-ligand binding residue prediction with protein language models: does the structure matter?Bioinformatics (Oxford, England) · 2025Article
- DescribePROT Database of Residue-Level Protein Structure and Function Annotations.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Drug Repurposing: Insights into Current Advances and Future Applications.Current medicinal chemistry · 2025Review
- Benzylidene Oxazolo[3,2-a]pyrimidine derivatives as promising anti-inflammatory agents: synthesis, quantum simulations, and molecular Docking.In silico pharmacology · 2025Article
- A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Identification of Marine Compounds Inhibiting NF-κBInducing Kinase Through Molecular Docking and Molecular Dynamics Simulations.Biomolecules · 2024Article
- Article
- Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures.Nature communications · 2024Article
- Article
- Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023Review
- xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures.Biomolecules · 2023Article
- Article
- GraphSite: Ligand Binding Site Classification with Deep Graph Learning.Biomolecules · 2022Article
- Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods.Drug discovery today · 2022Review
- Complementarity of the residue-level protein function and structure predictions in human proteins.Computational and structural biotechnology journal · 2022Article
- Development of Computational Approaches with a Fragment-Based Drug Design Strategy: In Silico Hsp90 Inhibitors Discovery.International journal of molecular sciences · 2021Article
- DescribePROT: database of amino acid-level protein structure and function predictions.Nucleic acids research · 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
- Heterologous expression and biochemical characterization of a thermostable endo-β-1,4-glucanase from Colletotrichum orchidophilum.Bioprocess and biosystems engineering · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein-ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein-ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein-ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.
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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.