ReviewBiochemistry2011
Efficient incorporation of protein flexibility and dynamics into molecular docking simulations.
Review in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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Who cites it
39 citing papers in PubMed, 102 citations in OpenAlex.
- Geometric Deep Learning-Based Drug Design Models for Small-Molecule Drug Discovery.Molecular informatics · 2026Review
- Transformer-accelerated discovery of inhibitors targeting the RpsAJournal of cheminformatics · 2026Article
- Binding Specificity and Local Frustration in Structure-based Drug Discovery.Current medicinal chemistry · 2026Review
- Unlocking the antimalarial potential of novel steroid-tetraoxane hybrids through consensus molecular docking and molecular dynamics investigation.Scientific reports · 2025Article
- STING activation by teniposide: a potential direct mechanism beyond cGAS stimulation.Frontiers in immunology · 2025Article
- Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling.Journal of chemical information and modeling · 2024Article
- Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.Scientific reports · 2022Article
- Tetrahydrocurcumin Has Similar Anti-Amyloid Properties as Curcumin: In Vitro Comparative Structure-Activity Studies.Antioxidants (Basel, Switzerland) · 2021Article
- Instantaneous generation of protein hydration properties from static structures.Communications chemistry · 2020Article
- MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment.Journal of chemical information and modeling · 2020Article
- Probing the local conformational flexibility in receptor recognition: mechanistic insight from an atomic-scale investigation.RSC advances · 2019Article
- Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer's Disease: A Computational Study.Marine drugs · 2018Article
- Article
- Development of inhibitors of receptor protein tyrosine phosphatase β/ζ (PTPRZ1) as candidates for CNS disorders.European journal of medicinal chemistry · 2018Article
- Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents.Marine drugs · 2017Article
- ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research.Journal of chemical information and modeling · 2017Article
- Dynamic Docking: A Paradigm Shift in Computational Drug Discovery.Molecules (Basel, Switzerland) · 2017Review
- Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.Current opinion in toxicology · 2017Article
- Ensemble Molecular Dynamics of a Protein-Ligand Complex: Residual Inhibitor Entropy Enhances Drug Potency in Butyrylcholinesterase.Bioenergetics : open access · 2017Article
- Exposing the Molecular Screening Method of Indonesian Natural Products Derivate as Drug Candidates for Cervical Cancer.Iranian journal of pharmaceutical research : IJPR · 2017Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Flexibility and dynamics are protein characteristics that are essential for the process of molecular recognition. Conformational changes in the protein that are coupled to ligand binding are described by the biophysical models of induced fit and conformational selection. Different concepts that incorporate protein flexibility into protein-ligand docking within the context of these two models are reviewed. Several computational studies that discuss the validity and possible limitations of such approaches will be presented. Finally, different approaches that incorporate protein dynamics, e.g., configurational entropy, and solvation effects into docking will be highlighted.
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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.