(Q35450396)

8 August 2017

title

Binding hotspots on K-ras: consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis (English)

1 reference

8 August 2017

1 reference

Priyanka Prakash

1

1 reference

8 August 2017

John F Hancock

series ordinal

2

1 reference

8 August 2017

Alemayehu A Gorfe

series ordinal

3

1 reference

8 August 2017

language of work or name

English

0 references

publication date

25 March 2015

1 reference

8 August 2017

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8 August 2017

volume

83

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8 August 2017

issue

5

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8 August 2017

page(s)

898-909

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Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras.

8 August 2017

cites work

1 reference

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12 July 2018

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Direct Ras Inhibitors Identified from a Structurally Rigidified Bicyclic Peptide Library

12 July 2018

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Ras nanoclusters: Versatile lipid-based signaling platforms

12 July 2018

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A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand

12 July 2018

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

12 July 2018

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Dragging ras back in the ring

12 July 2018

1 reference

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H-Ras forms dimers on membrane surfaces via a protein-protein interface.

12 July 2018

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12 July 2018

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K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions

12 July 2018

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Lessons from computer simulations of Ras proteins in solution and in membrane

12 July 2018

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Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function

12 July 2018

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In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction

12 July 2018

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Ras nanoclusters: a new drug target?

12 July 2018

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N-Ras forms dimers at POPC membranes

12 July 2018

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Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1

12 July 2018

1 reference

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Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

12 July 2018

1 reference

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Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

A comprehensive survey of Ras mutations in cancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-Mediated Activation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

The role of conserved waters in conformational transitions of Q61H K-ras

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Novel allosteric sites on Ras for lead generation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Inhibition of Ras for cancer treatment: the search continues

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

RAS oncogenes: weaving a tumorigenic web

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Analysis of Binding Site Hot Spots on the Surface of Ras GTPase

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Ras history: The saga continues

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations

12 July 2018

1 reference

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Conformational selection in G-proteins: lessons from Ras and Rho.

12 July 2018

1 reference

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Conformational states of human rat sarcoma (Ras) protein complexed with its natural ligand GTP and their role for effector interaction and GTP hydrolysis

12 July 2018

1 reference

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Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes

12 July 2018

1 reference

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Allosteric modulation of Ras positions Q61 for a direct role in catalysis

12 July 2018

1 reference

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Mechanisms of allostery and membrane attachment in Ras GTPases: implications for anti-cancer drug discovery

12 July 2018

1 reference

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Computational fragment-based binding site identification by ligand competitive saturation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Trapping moving targets with small molecules

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Binding site detection and druggability index from first principles.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Ras oncogenes: split personalities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

A novel switch region regulates H-ras membrane orientation and signal output

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Ras nanoclusters: molecular structure and assembly

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Plasma membrane nanoswitches generate high-fidelity Ras signal transduction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Scalable molecular dynamics with NAMD

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Druggability indices for protein targets derived from NMR-based screening data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Targeting RAS signalling pathways in cancer therapy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

The guanine nucleotide-binding switch in three dimensions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Formation of the Ras dimer is essential for Raf-1 activation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

VMD: visual molecular dynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

ras oncogenes in human cancer: a review

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Most human carcinomas of the exocrine pancreas contain mutant c-K-ras genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Detection of high incidence of K-ras oncogenes during human colon tumorigenesis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

A polybasic domain or palmitoylation is required in addition to the CAAX motif to localize p21ras to the plasma membrane

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

¹H, ¹³C and ¹⁵N resonance assignment for the human K-Ras at physiological pH.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4400267

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FPROT.24786

Metal-bis(2-picolyl)amine complexes as state 1(T) inhibitors of activated Ras protein

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25740554

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24786

1 reference

8 August 2017

1 reference

8 August 2017

1 reference