ReviewChemical biology & drug design2013
Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design.
Review in Chemical biology & drug design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
32 citing papers in PubMed.
- Molecular Simulations of Polymer-based Drug Nanocarriers: From Physical and Structural Properties to Controlled Release.Advanced healthcare materials · 2026Review
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Dual-site molecular glues for enhancing protein-protein interactions of the CDK12-DDB1 complex.Nature communications · 2024Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex.Current computer-aided drug design · 2021Article
- Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.BMC molecular and cell biology · 2019Article
- Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.Structure (London, England : 1993) · 2019Article
- Improving inverse docking target identification with Z-score selection.Chemical biology & drug design · 2019Article
- Pharmaceutical Machine Learning: Virtual High-Throughput Screens Identifying Promising and Economical Small Molecule Inhibitors of Complement Factor C1s.Biomolecules · 2018Article
- Article
- L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib.Chemical science · 2018Article
- Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders.Journal of chemical information and modeling · 2017Article
- Exploring Binding Mechanisms in Nuclear Hormone Receptors by Monte Carlo and X-ray-derived Motions.Biophysical journal · 2017Article
- A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces.Protein engineering, design & selection : PEDS · 2016Article
- MOLS 2.0: software package for peptide modeling and protein-ligand docking.Journal of molecular modeling · 2016Article
- Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment.Journal of chemical information and modeling · 2016Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays.Scientific reports · 2015Article
- A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.Molecules (Basel, Switzerland) · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules. In proteins, these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side-chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient's genetic makeup.
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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.