ArticleJournal of chemical theory and computation2017
Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- 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
- Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms.The journal of physical chemistry. B · 2024Article
- Applications of Molecular Dynamics Simulations in Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Article
- Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein.Structure (London, England : 1993) · 2022Article
- Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.New journal of chemistry = Nouveau journal de chimie · 2022Article
- Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations.Journal of chemical information and modeling · 2021Article
- 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
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
- Cosolvent Analysis Toolkit (CAT): a robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome.Scientific reports · 2019Article
- 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
- Solvents to Fragments to Drugs: MD Applications in Drug Design.Molecules (Basel, Switzerland) · 2018Review
- Allosteric Modulation of Intact γ-Secretase Structural Dynamics.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Membrane proteins represent a considerable fraction of pharmaceutical drug targets. A computational technique to identify ligand binding pockets in these proteins is therefore of great importance. We recently reported such a technique called pMD-membrane that utilizes small molecule probes to detect ligand binding sites and surface hotspots on membrane proteins based on probe-based molecular dynamics simulation. The current work extends pMD-membrane to a diverse set of small organic molecular species that can be used as cosolvents during simulation of membrane proteins. We also describe a projection technique for globally quantifying probe densities on the protein surface and introduce a technique to construct surface topography maps directly from the probe-binding propensity of surface residues. The map reveals surface patterns and geometric features that aid in filtering out high probe density hotspots lacking pocketlike characteristics. We demonstrate the applicability of the extended pMD-membrane and the new analysis tool by exploring the druggability of full-length G12D, G12V, and G13D oncogenic K-Ras mutants bound to a negatively charged lipid bilayer. Using data from 30 pMD-membrane runs conducted in the presence of a 2.8 M cosolvent made up of an equal proportion of seven small organic molecules, we show that our approach robustly identifies known allosteric ligand binding sites and other reactive regions on K-Ras. Our results also show that accessibility of some pockets is modulated by differential membrane interactions.
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What OpenQuestion holds
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.