Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

KRAS Dimerization Impacts MEK Inhibitor Sensitivity and Oncogenic Activity of Mutant KRAS

(2018) Chiara Ambrogio et al.   CELL

The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects

(2017) Christian W. Johnson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes

(2017) Suparna Sarkar-Banerjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

(2017) Nuria Plattner et al.   Nature Chemistry

Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants

(2017) Abdallah Sayyed-Ahmad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evolution of AF6-RAS association and its implications in mixed-lineage leukemia

(2017) Matthew J. Smith et al.   Nature Communications

Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis

(2016) Priyanka Prakash et al.   BIOPHYSICAL JOURNAL

The higher level of complexity of K-Ras4B activation at the membrane

(2016) Hyunbum Jang et al.   FASEB JOURNAL

Genetics and biology of pancreatic ductal adenocarcinoma

(2016) Haoqiang Ying et al.   GENES & DEVELOPMENT

K-RasV14I -induced Noonan syndrome predisposes to tumour development in mice

(2016) Isabel Hernández-Porras et al.   JOURNAL OF PATHOLOGY

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism

(2016) P. Lito et al.   SCIENCE

The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B

(2016) Shaoyong Lu et al.   Scientific Reports

Structure, Dynamics, Assembly, and Evolution of Protein Complexes

(2015) Joseph A. Marsh et al.   Annual Review of Biochemistry

High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site

(2015) Tanmay S. Chavan et al.   BIOPHYSICAL JOURNAL

GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site

(2015) Shaoyong Lu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations

(2015) J. C. Hunter et al.   MOLECULAR CANCER RESEARCH

Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

(2015) Matthew T Chang et al.   NATURE BIOTECHNOLOGY

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site

(2015) Mohammad T. Mazhab-Jafari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ras-GTP dimers activate the Mitogen-Activated Protein Kinase (MAPK) pathway

(2015) Xiaolin Nan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential dynamics of RAS isoforms in GDP- and GTP-bound states

(2015) Abhijeet Kapoor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GTP-Dependent K-Ras Dimerization

(2015) Serena Muratcioglu et al.   STRUCTURE

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Dragging Ras Back in the Ring

(2014) Andrew G. Stephen et al.   CANCER CELL

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins

(2014) Matteo Tiberti et al.   Journal of Chemical Information and Modeling

Integrated RAS signaling defined by parallel NMR detection of effectors and regulators

(2014) Matthew J Smith et al.   Nature Chemical Biology

In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C

(2014) J. C. Hunter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

K-RasV14Irecapitulates Noonan syndrome in mice

(2014) Isabel Hernández-Porras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

(2013) Albino Bacolla et al.   PLoS Genetics

A Comprehensive Survey of Ras Mutations in Cancer

(2012) I. A. Prior et al.   CANCER RESEARCH

Molecular Epidemiology of EGFR and KRAS Mutations in 3,026 Lung Adenocarcinomas: Higher Susceptibility of Women to Smoking-Related KRAS-Mutant Cancers

(2012) S. Dogan et al.   CLINICAL CANCER RESEARCH

Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome

(2012) Nathan T. Ihle et al.   JNCI-Journal of the National Cancer Institute

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

Separation-of-Function Mutants Unravel the Dual-Reaction Mode of Human 8-Oxoguanine DNA Glycosylase

(2011) Bjørn Dalhus et al.   STRUCTURE

Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders

(2010) Lothar Gremer et al.   HUMAN MUTATION

Conformational States of Human Rat Sarcoma (Ras) Protein Complexed with Its Natural Ligand GTP and Their Role for Effector Interaction and GTP Hydrolysis

(2010) Michael Spoerner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Mutation patterns in cancer genomes

(2009) A. F. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II

(2008) Benjamin Stieglitz et al.   EMBO JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY