Engineering extrinsic disorder to control protein activity in living cells

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch

(2016) Benjamin L Oakes et al.   NATURE BIOTECHNOLOGY

Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

(2016) Hayretin Yumerefendi et al.   Nature Chemical Biology

LOVTRAP: an optogenetic system for photoinduced protein dissociation

(2016) Hui Wang et al.   NATURE METHODS

Open source software for quantification of cell migration, protrusions, and fluorescence intensities

(2015) David J. Barry et al.   JOURNAL OF CELL BIOLOGY

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Design of protein switches based on an ensemble model of allostery

(2015) Jay H. Choi et al.   Nature Communications

Optogenetic approaches to cell migration and beyond

(2014) Matthew Weitzman et al.   CURRENT OPINION IN CELL BIOLOGY

CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries

(2014) Denis Tsygankov et al.   JOURNAL OF CELL BIOLOGY

Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

(2014) Robert Lindner et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms

(2014) P.-H. Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells

(2014) Dominik Niopek et al.   Nature Communications

Vav1 as a Central Regulator of Invadopodia Assembly

(2013) Gina L. Razidlo et al.   CURRENT BIOLOGY

ArchDB 2014: structural classification of loops in proteins

(2013) Jaume Bonet et al.   NUCLEIC ACIDS RESEARCH

MISTIC: mutual information server to infer coevolution

(2013) Franco L. Simonetti et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Rational design of a ligand-controlled protein conformational switch

(2013) O. Dagliyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arp2/3 Is Critical for Lamellipodia and Response to Extracellular Matrix Cues but Is Dispensable for Chemotaxis

(2012) Congying Wu et al.   CELL

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

(2012) David Shirvanyants et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optical Control of Protein Activity by Fluorescent Protein Domains

(2012) X. X. Zhou et al.   SCIENCE

An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching

(2011) Michele L. Markwardt et al.   PLoS One

High Cleavage Efficiency of a 2A Peptide Derived from Porcine Teschovirus-1 in Human Cell Lines, Zebrafish and Mice

(2011) Jin Hee Kim et al.   PLoS One

High-Resolution Quantification of Focal Adhesion Spatiotemporal Dynamics in Living Cells

(2011) Mathew E. Berginski et al.   PLoS One

Integration, scaling, space-group assignment and post-refinement

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

Features and development ofCoot

(2010) P. Emsley et al.   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

Endogenous RhoG Is Rapidly Activated after Epidermal Growth Factor Stimulation through Multiple Guanine-Nucleotide Exchange Factors

(2010) Thomas Samson et al.   MOLECULAR BIOLOGY OF THE CELL

Engineered allosteric activation of kinases in living cells

(2010) Andrei V Karginov et al.   NATURE BIOTECHNOLOGY

Bright cyan fluorescent protein variants identified by fluorescence lifetime screening

(2010) Joachim Goedhart et al.   NATURE METHODS

Rapid blue-light–mediated induction of protein interactions in living cells

(2010) Matthew J Kennedy et al.   NATURE METHODS

Automated minimization of steric clashes in protein structures

(2010) Srinivas Ramachandran et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Designing switchable enzymes

(2009) Marc Ostermeier   CURRENT OPINION IN STRUCTURAL BIOLOGY

DAMMIF, a program for rapidab-initioshape determination in small-angle scattering

(2009) Daniel Franke et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Spatiotemporal control of cell signalling using a light-switchable protein interaction

(2009) Anselm Levskaya et al.   NATURE

Coordination of Rho GTPase activities during cell protrusion

(2009) Matthias Machacek et al.   NATURE

A genetically encoded photoactivatable Rac controls the motility of living cells

(2009) Yi I. Wu et al.   NATURE

Estimation of the available free energy in a LOV2-Jα photoswitch

(2008) Xiaolan Yao et al.   Nature Chemical Biology

Protein dynamics under light control

(2008) Michele Vendruscolo   Nature Chemical Biology

Surface Sites for Engineering Allosteric Control in Proteins

(2008) J. Lee et al.   SCIENCE

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE