PRL‐dock: Protein‐ligand docking based on hydrogen bond matching and probabilistic relaxation labeling
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Summary
A novel docking technique based on hydrogen bond matching and probabilistic relaxation labeling that deals with multiple hydrogen bonds and can match many acceptors and donors simultaneously is presented.
- Type
- article
- Published
- 2012-08-01
- Cited by
- 43
- References
- 58
- OpenAlex
- https://openalex.org/W1972881359
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:25902044
Keywords
Hydrogen bond, van der Waals force, Docking (animal), Chemistry, Intermolecular force
References
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- Scene Labeling by Relaxation Operations
- Searching Protein Three-Dimensional Structures in Faster Than Linear Time
- Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
- F^2Dock: Fast Fourier Protein-Protein Docking
- Outstanding challenges in protein–ligand docking and structure‐based virtual screening
- Advances and Challenges in Protein-Ligand Docking
- Ligand docking to proteins with discrete side-chain flexibility.
- Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking.
- PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures
- A geometry-based suite of molecular docking processes.
- A probabilistic relaxation labeling framework for reducing the noise effect in geometric biclustering of gene expression data
- Development and validation of a genetic algorithm for flexible docking.
Cited by
- The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures.
- Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
- An efficient searching algorithm based on local shape complementarity of hydrogen bonds and relaxation labeling for protein-ligand docking
- A quadratic penalty method for hypergraph matching
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development
- MOLECULAR DOCKING STUDIES OF PHYTOCONSTITUENTS ISOLATED FROM POLYGONUM GLABRUM AND BUDDLEJA ASIATICA
- Hydrogen bond analysis of the EGFR-ErbB3 heterodimer related to non-small cell lung cancer and drug resistance.
- Investigation of Cyclobenzaprine Interactions with P450 Cytochromes CYP1A2 and CYP3A4 through Molecular Docking Tools
- A unified formulation of a class of graph matching techniques
- The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major May Be Involved in the Resistance to Drugs such as Paromomycin
- An Improved Protein-Protein Docking Technique Using Multilevel Scoring Function
- Stability Investigation Using Hydrogen Bonds for Different Mutations and Drug Resistance in Non-Small Cell Lung Cancer Patients
- Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (Ocimum basilicum L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study
- Computer-Aided Identification of Bioactive compounds of Azadirachta indica (Neem) with Potential activity against SARS-CoV-2 main protease
- Computational screening of phytochemicals from three medicinal plants as inhibitors of transmembrane protease serine 2 implicated in SARS-CoV-2 infection
- Mangiferin: Analgesic properties in neuropathic pain, molecular docking and meta-analysis
- Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach
- In silico investigation of possible caffeine interactions with common inflammation-related targets
- In vitro dual activity of Aloe marlothii roots and its chemical constituents against Plasmodium falciparum asexual and sexual stage parasites.
- Preclinical insights into fucoidan as a nutraceutical compound against perfluorooctanoic acid-associated obesity via targeting endoplasmic reticulum stress
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