ArticleMolecular simulation
Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras.
Article in Molecular simulation. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Time-Resolved Crystallography Reveals the Mechanisms of GTP hydrolysis for N-RAS and the Oncogenic Mutants G12C, G12V and Q61L.bioRxiv : the preprint server for biology · 2025Article
- Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.The journal of physical chemistry. B · 2022Article
- Activation Mechanism of RhoA Caused by Constitutively Activating Mutations G14V and Q63L.International journal of molecular sciences · 2022Article
- A regulatory role of membrane by direct modulation of the catalytic kinase domain.Small GTPases · 2021Review
- Unveiling the Dynamics of KRAS4b on Lipid Model Membranes.The Journal of membrane biology · 2021Article
- Approaches to inhibiting oncogenic K-Ras.Small GTPases · 2021Review
- Comparative MD simulations and advanced analytics based studies on wild-type and hot-spot mutant A59G HRas.PloS one · 2020Article
- Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding.ACS omega · 2019Article
- Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions.Scientific reports · 2017Article
- Review: Translational GTPases.Biopolymers · 2016Review
- Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis.Biophysical journal · 2016Article
- pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.PLoS computational biology · 2015Article
- Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis.Proteins · 2015Article
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Authors and funding
2 authors.
Funding
Abstract
Over the last 40 years, we have learnt a great deal about the Ras onco-proteins. These intracellular molecular switches are essential for the function of a variety of physiological processes, including signal transduction cascades responsible for cell growth and proliferation. Molecular simulations and free energy calculations have played an essential role in elucidating the conformational dynamics and energetics underlying the GTP hydrolysis reaction catalysed by Ras. Here we present an overview of the main lessons from molecular simulations on the GTPase reaction and conformational dynamics of this important anti-cancer drug target. In the first part, we summarise insights from quantum mechanical and combined quantum mechanical/molecular mechanical simulations as well as other free energy methods and highlight consensus viewpoints as well as remaining controversies. The second part provides a very brief overview of new insights emerging from large-scale molecular dynamics simulations. We conclude with a perspective regarding future studies of Ras where computational approaches will likely play an active role.
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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.