Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis

Effects of Disulfide Bonds on Bindings of Inhibitors to BACE1 Decoded by Multiple Replica Accelerated Molecular Dynamics Simulations

(2020) Jianzhong Chen et al.   ACS Chemical Neuroscience

Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases

(2020) Khuchtumur Bum-Erdene et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations

(2020) Aman Chandra Kaushik et al.   BRIEFINGS IN BIOINFORMATICS

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding

(2020) Jinan Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry

(2020) Xubo Lin et al.   JOURNAL OF CHEMICAL PHYSICS

Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions

(2020) Yuwei Zhang et al.   Journal of Chemical Theory and Computation

Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics

(2020) Jianzhong Chen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds

(2019) Abimael Cruz-Migoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-Specific Oncogenic Activity of KRASA146T

(2019) Emily J. Poulin et al.   Cancer Discovery

Structural basis of the atypical activation mechanism of KRAS V14I

(2019) Asim K. Bera et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors

(2019) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations

(2019) Jianzhong Chen et al.   NUCLEIC ACIDS RESEARCH

Drugging an undruggable pocket on KRAS

(2019) Dirk Kessler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deactivation Pathway of Ras GTPase Underlies Conformational Substates as Targets for Drug Design

(2019) Shaoyong Lu et al.   ACS Catalysis

1H, 15N backbone assignment and comparative analysis of the wild type and G12C, G12D, G12V mutants of K-Ras bound to GDP at physiological pH

(2019) Gyula Pálfy et al.   Biomolecular NMR Assignments

Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis

(2019) Mohammed Khaled et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations

(2019) Yan Xu et al.   Journal of Physical Chemistry Letters

Lipid Acyl Chain cis Double Bond Position Modulates Membrane Domain Registration/Anti-Registration

(2019) Siya Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D

(2019) Christian W. Johnson et al.   Cell Reports

Molecular Mechanism of Binding Selectivity of Inhibitors toward BACE1 and BACE2 Revealed by Multiple Short Molecular Dynamics Simulations and Free-Energy Predictions

(2019) Jianzhong Chen et al.   ACS Chemical Neuroscience

The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity

(2019) Jude Canon et al.   NATURE

Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer

(2019) G. Aaron Hobbs et al.   Cancer Discovery

Oncogenic G12D mutation alters local conformations and dynamics of K-Ras

(2019) Sezen Vatansever et al.   Scientific Reports

Computational Design of Myristoylated Cell-Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector-Binding Membrane Interface

(2019) Zhenlu Li et al.   Journal of Chemical Information and Modeling

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange

(2018) Chimno I. Nnadi et al.   Journal of Chemical Information and Modeling

K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D

(2018) Jillian A. Parker et al.   STRUCTURE

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

(2018) Tatu Pantsar et al.   PLoS Computational Biology

Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs

(2018) Priyanka Prakash et al.   BIOPHYSICAL JOURNAL

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

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

The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins

(2017) Dong Song et al.   Journal of Chemical Information and Modeling

Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations

(2017) Guodong Hu et al.   Journal of Chemical Information and Modeling

Molecular genetics and cellular events of K-Ras-driven tumorigenesis

(2017) G G Jinesh et al.   ONCOGENE

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

Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras

(2017) Shenyuan Xu et al.   Acta Crystallographica Section D-Structural Biology

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

(2016) Priyanka Prakash et al.   BIOPHYSICAL JOURNAL

Ras Conformational Ensembles, Allostery, and Signaling

(2016) Shaoyong Lu et al.   CHEMICAL REVIEWS

Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

(2016) Shaoyong Lu et al.   CHEMICAL SOCIETY REVIEWS

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1

(2016) Huiyong Sun et al.   Journal of Chemical Theory and Computation

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

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

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

(2016) Shaoyong Lu et al.   Scientific Reports

Redox-Responsive Fluorescent Probes with Different Design Strategies

(2015) Zhangrong Lou et al.   ACCOUNTS OF CHEMICAL RESEARCH

Tyrosine phosphorylation of RAS by ABL allosterically enhances effector binding

(2015) Pamela Y. Ting et al.   FASEB JOURNAL

A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods

(2015) Jianzhong Chen et al.   Journal of Chemical Information and Modeling

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier 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

Quantitative prediction of charge mobilities of π-stacked systems by first-principles simulation

(2015) Wei-Qiao Deng et al.   Nature Protocols

PLIP: fully automated protein–ligand interaction profiler

(2015) Sebastian Salentin et al.   NUCLEIC ACIDS RESEARCH

How do K-RAS-activated cells evade cellular defense mechanisms?

(2015) Y-S Lee et al.   ONCOGENE

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

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD

(2015) Susan K. Fetics et al.   STRUCTURE

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Small-molecule modulation of Ras signaling

(2014) Jochen Spiegel et al.   Nature Chemical Biology

Src promotes GTPase activity of Ras via tyrosine 32 phosphorylation

(2014) S. Bunda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

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

(2013) Jonathan M. Ostrem et al.   NATURE

Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function

(2013) H. J. Hocker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Comprehensive Survey of Ras Mutations in Cancer

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

Specific Conformational States of Ras GTPase upon Effector Binding

(2012) Julie Baussand et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2011) Mitsugu Araki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

Allosteric Modulation of Ras-GTP Is Linked to Signal Transduction through RAF Kinase

(2010) Greg Buhrman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) G. Buhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

(2010) Suryani Lukman et al.   PLoS Computational Biology

Mechanisms of Allostery and Membrane Attachment in Ras GTPases: Implications for Anti-Cancer Drug Discovery

(2009) A. Gorfe   CURRENT MEDICINAL CHEMISTRY

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study

(2008) Emilia L. Wu et al.   CHEMISTRY-A EUROPEAN JOURNAL

Ras oncogenes: split personalities

(2008) Antoine E. Karnoub et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins

(2008) Alemayehu A. Gorfe et al.   STRUCTURE