Published in J Comput Chem on November 30, 2004
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp. Biophys J (2006) 1.89
Progress in the prediction of pKa values in proteins. Proteins (2011) 1.36
Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. Proc Natl Acad Sci U S A (2012) 1.29
Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease. Biochemistry (2010) 1.11
Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations. Biochim Biophys Acta (2006) 1.11
Brownian dynamics simulation of protein solutions: structural and dynamical properties. Biophys J (2010) 1.07
On the role of electrostatics in protein-protein interactions. Phys Biol (2011) 1.04
Rapid calculation of protein pKa values using Rosetta. Biophys J (2012) 0.90
14-3-3ζ interacts with stat3 and regulates its constitutive activation in multiple myeloma cells. PLoS One (2012) 0.88
Computational studies of difference in binding modes of peptide and non-peptide inhibitors to MDM2/MDMX based on molecular dynamics simulations. Int J Mol Sci (2012) 0.88
Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT. J Comput Aided Mol Des (2009) 0.87
Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment. J Phys Chem B (2006) 0.85
Binding affinity prediction for ligands and receptors forming tautomers and ionization species: inhibition of mitogen-activated protein kinase-activated protein kinase 2 (MK2). J Med Chem (2012) 0.79
Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure. Eur Phys J E Soft Matter (2010) 0.78
Development and testing of a general amber force field. J Comput Chem (2004) 23.29
Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model (2006) 7.93
A medicinal chemist's guide to molecular interactions. J Med Chem (2010) 3.39
Fluorine in medicinal chemistry. Chembiochem (2004) 3.25
Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model (2008) 2.04
Validation and use of the MM-PBSA approach for drug discovery. J Med Chem (2005) 1.90
Intramolecular hydrogen bonding in medicinal chemistry. J Med Chem (2010) 1.75
Computational alanine scanning of the 1:1 human growth hormone-receptor complex. J Comput Chem (2002) 1.62
Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. Science (2003) 1.37
Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. Proteins (2002) 1.36
Multiscale contrast enhancement for radiographies: Laplacian Pyramid versus fast wavelet transform. IEEE Trans Med Imaging (2002) 1.24
Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J Med Chem (2002) 1.23
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers (2003) 1.21
Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J Mol Model (2003) 1.20
Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. J Med Chem (2003) 1.15
New-generation amber united-atom force field. J Phys Chem B (2006) 1.11
An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application. J Chem Inf Model (2005) 1.09
Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. J Mol Graph Model (2004) 1.05
Chemical fragment spaces for de novo design. J Chem Inf Model (2007) 1.04
Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations. J Chem Inf Model (2007) 1.03
SIGIRR, a negative regulator of TLR/IL-1R signalling promotes Microbiota dependent resistance to colonization by enteric bacterial pathogens. PLoS Pathog (2013) 1.02
Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. J Med Chem (2003) 0.99
Comparison of the binding pockets of two chemically unrelated allosteric antagonists of the mGlu5 receptor and identification of crucial residues involved in the inverse agonism of MPEP. J Neurochem (2006) 0.98
Conformational preferences of substituted prolines in the collagen triple helix. Biopolymers (2002) 0.98
Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J Med Chem (2005) 0.96
Rationalizing tight ligand binding through cooperative interaction networks. J Chem Inf Model (2011) 0.95
Design of novel aminopyrrolidine factor Xa inhibitors from a screening hit. Eur J Med Chem (2009) 0.94
A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. Biophys J (2002) 0.92
Oxidosqualene cyclase second-sphere residues profoundly influence the product profile. Chembiochem (2004) 0.91
Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin. J Org Chem (2002) 0.90
Tyramine fragment binding to BACE-1. Bioorg Med Chem Lett (2008) 0.88
Focused library design in GPCR projects on the example of 5-HT(2c) agonists: comparison of structure-based virtual screening with ligand-based search methods. Proteins (2005) 0.88
Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study. J Org Chem (2006) 0.86
Phenotypic screening of a targeted mutant library reveals Campylobacter jejuni defenses against oxidative stress. Infect Immun (2014) 0.85
pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step. J Comput Chem (2002) 0.85
CONFECT: conformations from an expert collection of torsion patterns. ChemMedChem (2013) 0.84
From astemizole to a novel hit series of small-molecule somatostatin 5 receptor antagonists via GPCR affinity profiling. J Med Chem (2007) 0.83
Dose-dependent antithrombotic activity of an orally active tissue factor/factor VIIa inhibitor without concomitant enhancement of bleeding propensity. Bioorg Med Chem (2006) 0.82
Torsion angle preferences in druglike chemical space: a comprehensive guide. J Med Chem (2013) 0.80
Discovery of a factor Xa inhibitor (3R,4R)-1-(2,2-difluoro-ethyl)-pyrrolidine-3,4-dicarboxylic acid 3-[(5-chloro-pyridin-2-yl)-amide] 4-[[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenyl]-amide] as a clinical candidate. Bioorg Med Chem Lett (2010) 0.80
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach. J Comput Chem (2003) 0.79
Design of libraries targeting protein-protein interfaces. ChemMedChem (2013) 0.79
The Serine Protease Autotransporter Pic Modulates Citrobacter rodentium Pathogenesis and Its Innate Recognition by the Host. Infect Immun (2015) 0.79
Insights into the mode of action of benzyl isothiocyanate on Campylobacter jejuni. Appl Environ Microbiol (2013) 0.79
Selective and orally bioavailable phenylglycine tissue factor/factor VIIa inhibitors. Bioorg Med Chem Lett (2005) 0.78
The environment of amide groups in protein-ligand complexes: H-bonds and beyond. J Mol Model (2005) 0.78
Ensemble methods for classification in cheminformatics. J Chem Inf Comput Sci (2004) 0.78
3-Amino-pyrazolo[3,4-d]pyrimidines as p38α kinase inhibitors: design and development to a highly selective lead. Bioorg Med Chem Lett (2011) 0.77
Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. J Comput Chem (2003) 0.76
Computational medicinal chemistry. J Med Chem (2010) 0.75
Prediction of UV and ESI-MS signal intensities. J Chem Inf Model (2005) 0.75
Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement. J Am Chem Soc (2002) 0.75
Mechanistic insights into oxidosqualene cyclizations through homology modeling. J Comput Chem (2003) 0.75