ArticleJournal of chemical information and modeling2015
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.
Article in Journal of chemical information and modeling, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Quantum Biochemistry Insights into Ligand Recognition at the aACS omega · 2026Article
- Identification of Novel Extracellular-Signal-Regulated Kinase 2 Inhibitors Through Machine Learning-Driven De Novo Design, Molecular Docking, and Free-Energy Perturbation.Pharmaceuticals (Basel, Switzerland) · 2026Article
- PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.Nucleic acids research · 2025Article
- Functional and Structure Prediction of Hypothetical Proteins FromBioMed research international · 2025Article
- Article
- Mce1R of Mycobacterium tuberculosis prefers long-chain fatty acids as specific ligands: a computational study.Molecular diversity · 2023Article
- Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.Journal of chemical information and modeling · 2023Article
- Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking.Foods (Basel, Switzerland) · 2021Article
- Identification of a Novel Therapeutic Target against XDRMicroorganisms · 2021Article
- LmjF.36.3850, a novel hypothetical Leishmania major protein, contributes to the infection.Immunology · 2021Article
- Comparative Metabolic Pathways Analysis and Subtractive Genomics Profiling to Prioritize Potential Drug Targets AgainstFrontiers in microbiology · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLMolecules (Basel, Switzerland) · 2020Article
- Loop Grafting between Similar Local Environments for Fc-Silent Antibodies.Journal of chemical information and modeling · 2020Article
- Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.Nature methods · 2020Article
- Conformational Studies of Glucose Transporter 1 (GLUT1) as an Anticancer Drug Target.Molecules (Basel, Switzerland) · 2019Article
- Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin.Molecules (Basel, Switzerland) · 2018Article
- Analgesic Activity, Chemical Profiling and Computational Study onFrontiers in pharmacology · 2018Article
- Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins.Scientific reports · 2017Article
- Elucidating a chemical defense mechanism of Antarctic sponges: A computational study.Journal of molecular graphics & modelling · 2017Article
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Authors and funding
7 authors.
Funding
Abstract
Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.
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