SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Imaging ultrafast molecular dynamics with laser-induced electron diffraction

(2012) Cosmin I. Blaga et al.   NATURE

Molecular origin of differences in hole and electron mobility in amorphous Alq3—a multiscale simulation study

(2012) Andreas Fuchs et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

(2012) N. P. King et al.   SCIENCE

High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale

(2011) Allard J. Katan et al.   CELL

Derivatives of molecular surface area and volume: Simple and exact analytical formulas

(2011) Konstantin V. Klenin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Crystal Structure of Sol i 2: A Major Allergen from Fire Ant Venom

(2011) Aline S. Borer et al.   JOURNAL OF MOLECULAR BIOLOGY

Deposition of Palladium Nanoparticles on Self-Assembled, Zinc-Induced Tubulin Macrotubes and Sheets

(2011) Silke Behrens   JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY

Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo

(2011) Timo Strunk et al.   MOLECULAR MICROBIOLOGY

Receptor flexibility in small-molecule docking calculations

(2011) Daria B. Kokh et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Selective Dispersion of Single-Walled Carbon Nanotubes with Specific Chiral Indices by Poly(N-decyl-2,7-carbazole)

(2010) Fabien A. Lemasson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Molecular Understanding of Organic Solar Cells: The Challenges

(2009) Jean-Luc Brédas et al.   ACCOUNTS OF CHEMICAL RESEARCH

Folding Path and Funnel Scenarios for Two Small Disulfide-Bridged Proteins

(2009) Ivan Kondov et al.   BIOCHEMISTRY

A Free-Energy Approach for All-Atom Protein Simulation

(2009) Abhinav Verma et al.   BIOPHYSICAL JOURNAL

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Template-free protein structure prediction and quality assessment with an all-atom free-energy model

(2009) Srinivasa Murthy Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

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

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

Flexible Side Chain Models Improve Enrichment Rates in In Silico Screening

(2008) Daria B. Kokh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Simulating charge transport in tris(8-hydroxyquinoline) aluminium (Alq3)

(2008) J. J. Kwiatkowski et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE