The lac Repressor Displays Facilitated Diffusion in Living Cells

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

An end to 40 years of mistakes in DNA–protein association kinetics?

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Structural origins for selectivity and specificity in an engineered bacterial repressor-inducer pair

(2009) Michael A. Klieber et al.   FEBS Journal

Effects of macromolecular crowding and DNA looping on gene regulation kinetics

(2009) Gene-Wei Li et al.   Nature Physics

Nonspecifically bound proteins spin while diffusing along DNA

(2009) Paul C Blainey et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA

(2008) Isabelle Bonnet et al.   NUCLEIC ACIDS RESEARCH

Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1

(2008) M. Doucleff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation