Published in Chem Rev on May 01, 2006
An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins (2009) 2.44
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Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
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Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des (2011) 1.13
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Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem (2013) 0.93
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Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, III: Molecular dynamics simulation incorporating a cyanophenylalanine spectroscopic probe. Biophys J (2009) 0.92
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An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions. J Comput Chem (2010) 0.87
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Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering. Protein Sci (2014) 0.85
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Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. J Chem Theory Comput (2015) 0.82
A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces. J Math Anal Appl (2008) 0.81
Exploiting conformational dynamics in drug discovery: design of C-terminal inhibitors of Hsp90 with improved activities. J Chem Inf Model (2014) 0.81
Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations. Biophys J (2014) 0.81
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Analysis of sub-tauc and supra-tauc motions in protein Gbeta1 using molecular dynamics simulations. Biophys J (2009) 0.80
Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. J Mol Model (2014) 0.80
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Coarse-Grained Models for Protein-Cell Membrane Interactions. Polymers (Basel) (2015) 0.80
SIMS: a hybrid method for rapid conformational analysis. PLoS One (2013) 0.80
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Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process. J Phys Chem B (2015) 0.80
Functional loop dynamics of the streptavidin-biotin complex. Sci Rep (2015) 0.80
Predicting protein ligand binding motions with the conformation explorer. BMC Bioinformatics (2011) 0.80
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Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. Monatsh Chem (2016) 0.79
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Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. J Am Chem Soc (2005) 1.19
Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophys J (2007) 1.18
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers (2004) 1.18
Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc (2010) 1.18
Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. J Am Chem Soc (2002) 1.17
Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain. J Mol Biol (2007) 1.17
Ligand-induced conformational change in the alpha7 nicotinic receptor ligand binding domain. Biophys J (2005) 1.17
Asymmetric structural motions of the homomeric alpha7 nicotinic receptor ligand binding domain revealed by molecular dynamics simulation. Biophys J (2003) 1.17
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol (2006) 1.17
On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci (2003) 1.17
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol (2011) 1.16
Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J Am Chem Soc (2004) 1.16
H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc (2007) 1.16
Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J Am Chem Soc (2006) 1.15
Towards an in vivo biologically inspired nanofactory. Nat Nanotechnol (2007) 1.15
Structural and dynamic properties of water around acetylcholinesterase. Protein Sci (2002) 1.15
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry (2011) 1.14
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A (2007) 1.14
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14
Restrained molecular dynamics simulations of HIV-1 protease: the first step in validating a new target for drug design. Biopolymers (2006) 1.14
Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach. J Phys Chem B (2007) 1.14