ArticlePLoS computational biology2015
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.Journal of chemical information and modeling · 2024Article
- Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants.Protein science : a publication of the Protein Society · 2024Review
- Article
- Application of Mixed-Solvent Molecular Dynamics Simulations for Prediction of Allosteric Sites on G Protein-Coupled Receptors.Molecular pharmacology · 2023Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Approaches to inhibiting oncogenic K-Ras.Small GTPases · 2021Review
- Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Biology, pathology, and therapeutic targeting of RAS.Advances in cancer research · 2020Review
- Exploring the computational methods for protein-ligand binding site prediction.Computational and structural biotechnology journal · 2020Review
- Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation.The journal of physical chemistry. B · 2019Article
- Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis.The journal of physical chemistry. B · 2019Article
- Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding.ACS omega · 2019Article
- Article
- Article
- Review
- Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification.Journal of chemical theory and computation · 2017Article
- Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers.Scientific reports · 2017Article
- Inhibition of prenylated KRAS in a lipid environment.PloS one · 2017Article
- Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics.Journal of medicinal chemistry · 2016Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.
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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.