Deconstruction of the Ras switching cycle through saturation mutagenesis

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

Origins of Allostery and Evolvability in Proteins: A Case Study

(2016) Arjun S. Raman et al.   CELL

RAS isoforms and mutations in cancer at a glance

(2016) G. Aaron Hobbs et al.   JOURNAL OF CELL SCIENCE

K-Ras protein as a drug target

(2016) Frank McCormick   JOURNAL OF MOLECULAR MEDICINE-JMM

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

(2016) Shaoyong Lu et al.   Scientific Reports

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

‘Latent drivers’ expand the cancer mutational landscape

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Structure and Function: Looking through the Network of Side-Chain Interactions

(2015) Moitrayee Bhattacharyya et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Tyrosine phosphorylation of RAS by ABL allosterically enhances effector binding

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

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing

(2014) Arti Tripathi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

(2014) J. I. Boucher et al.   GENETICS

A universal cloning method based on yeast homologous recombination that is simple, efficient, and versatile

(2014) Tammy M. Joska et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

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

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

(2014) L. Iversen et al.   SCIENCE

Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda

(2014) Andrey A. Lebedev et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Genomic and Cellular Foundations of Animal Origins

(2013) Daniel J. Richter et al.   Annual Review of Genetics

Differences in the Regulation of K-Ras and H-Ras Isoforms by Monoubiquitination

(2013) Rachael Baker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

An automated approach to network features of protein structure ensembles

(2013) Moitrayee Bhattacharyya et al.   PROTEIN SCIENCE

Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1

(2013) Jeffrey S Iwig et al.   eLife

Collaboration gets the most out of software

(2013) Andrew Morin et al.   eLife

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

(2013) Stephen R Fairclough et al.   GENOME BIOLOGY

Characterization of the Second Ion-Binding Site in the G Domain of H-Ras

(2012) Casey O’Connor et al.   BIOCHEMISTRY

Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

(2012) Genevieve Holzapfel et al.   BIOCHEMISTRY

A Comprehensive Survey of Ras Mutations in Cancer

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

The Ras protein superfamily: Evolutionary tree and role of conserved amino acids

(2012) Ana Maria Rojas et al.   JOURNAL OF CELL BIOLOGY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Genomic and Biological Characterization of Exon 4 KRAS Mutations in Human Cancer

(2010) M. Janakiraman et al.   CANCER RESEARCH

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

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

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pseudo-merohedral twinning in monoclinic crystals of wild-type human brain neuroglobin

(2009) Djemel Hamdane et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Selecting optimal second-line tyrosine kinase inhibitor therapy for chronic myeloid leukemia patients after imatinib failure: does the BCR-ABL mutation status really matter?

(2009) S. Branford et al.   BLOOD

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

(2009) Jayajit Das et al.   CELL

Improved Binding of Raf to Ras·GDP Is Correlated with Biological Activity

(2009) Christina Kiel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

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

(2008) Daniel Abankwa et al.   EMBO JOURNAL

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Membrane-dependent signal integration by the Ras activator Son of sevenless

(2008) Jodi Gureasko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2008) Alemayehu A. Gorfe et al.   STRUCTURE