Published in Proteins on December 01, 2004
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem (2010) 8.79
Pharmacological recruitment of aldehyde dehydrogenase 3A1 (ALDH3A1) to assist ALDH2 in acetaldehyde and ethanol metabolism in vivo. Proc Natl Acad Sci U S A (2015) 0.91
Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Biochemistry (2007) 0.88
Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme. J Biol Chem (2011) 0.86
Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate. J Biol Chem (2013) 0.80
TraeALDH7B1-5A, encoding aldehyde dehydrogenase 7 in wheat, confers improved drought tolerance in Arabidopsis. Planta (2015) 0.77
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. J Chem Theory Comput (2012) 5.57
Additive empirical force field for hexopyranose monosaccharides. J Comput Chem (2008) 3.23
A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem (2004) 2.79
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. J Chem Theory Comput (2009) 2.61
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol (2005) 1.99
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput (2012) 1.93
Domain swapping is a consequence of minimal frustration. Proc Natl Acad Sci U S A (2004) 1.93
Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput (2007) 1.86
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
Polarizable empirical force field for aromatic compounds based on the classical drude oscillator. J Phys Chem B (2007) 1.77
Differential tensile strength and collagen composition in ascending aortic aneurysms by aortic valve phenotype. Ann Thorac Surg (2013) 1.71
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol. J Chem Theory Comput (2009) 1.68
Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochemistry (2004) 1.62
The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol (2005) 1.60
Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc (2009) 1.54
Stabilizing IkappaBalpha by "consensus" design. J Mol Biol (2006) 1.53
CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling. J Chem Theory Comput (2011) 1.51
Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proc Natl Acad Sci U S A (2005) 1.42
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. J Phys Chem Lett (2011) 1.41
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose. J Phys Chem B (2009) 1.40
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.39
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy. Biophys J (2008) 1.30
NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases. J Am Chem Soc (2006) 1.29
Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput (2007) 1.28
Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J Chem Inf Model (2011) 1.26
Identification of novel extracellular signal-regulated kinase docking domain inhibitors. J Med Chem (2005) 1.25
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field. J Chem Theory Comput (2010) 1.24
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J Comput Chem (2009) 1.22
Characterization of an alarm pheromone secreted by amphibian tadpoles that induces behavioral inhibition and suppression of the neuroendocrine stress axis. Horm Behav (2009) 1.14
CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field. J Comput Chem (2005) 1.13
Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding. J Phys Chem A (2006) 1.13
Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem (2008) 1.11
Recent Developments and Applications of the CHARMM force fields. Wiley Interdiscip Rev Comput Mol Sci (2011) 1.09
Tyrosine sulfation is prevalent in human chemokine receptors important in lung disease. Am J Respir Cell Mol Biol (2008) 1.09
Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter. J Med Chem (2010) 1.07
Many-body polarization effects and the membrane dipole potential. J Am Chem Soc (2009) 1.06
Minimal models for proteins and RNA from folding to function. Prog Mol Biol Transl Sci (2008) 1.05
Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers. J Mol Model (2009) 1.04
Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates. Mol Pharm (2010) 1.01
Computational ligand-based rational design: Role of conformational sampling and force fields in model development. Medchemcomm (2011) 1.01
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates. J Chem Theory Comput (2011) 1.00
Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II. PLoS Pathog (2013) 0.97
Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr Comput Aided Drug Des (2011) 0.97
Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases. J Am Chem Soc (2009) 0.94
Development of an empirical force field for silica. Application to the quartz-water interface. J Phys Chem B (2006) 0.94
Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor. Nucleic Acids Res (2012) 0.93
The Class D beta-lactamase family: residues governing the maintenance and diversity of function. Protein Eng Des Sel (2011) 0.90
Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin. ACS Med Chem Lett (2012) 0.89
Inhibition requirements of the human apical sodium-dependent bile acid transporter (hASBT) using aminopiperidine conjugates of glutamyl-bile acids. Pharm Res (2009) 0.89
Impact of ribosomal modification on the binding of the antibiotic telithromycin using a combined grand canonical monte carlo/molecular dynamics simulation approach. PLoS Comput Biol (2013) 0.88
Polarizable empirical force field for acyclic polyalcohols based on the classical drude oscillator. Biopolymers (2013) 0.88
Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Biochemistry (2007) 0.88
Mitogen activated protein (MAP) kinases: development of ATP and non-ATP dependent inhibitors. Med Chem (2006) 0.88
Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J Chem Theory Comput (2012) 0.88
Design of Inhibitors for S100B. Curr Top Med Chem (2005) 0.88
Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes. Mol Pharm (2008) 0.87
PM3-compatible zinc parameters optimized for metalloenzyme active sites. J Comput Chem (2004) 0.87
Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study. J Phys Chem B (2008) 0.86
Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures. Nucleic Acids Res (2012) 0.86
Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies. J Mol Biol (2011) 0.86
Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations. J Am Chem Soc (2011) 0.85
Targeting protein tyrosine phosphatase SHP2 for the treatment of PTPN11-associated malignancies. Mol Cancer Ther (2013) 0.85
Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement. J Med Chem (2010) 0.85
Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade. J Med Chem (2011) 0.84
Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. J Phys Chem B (2010) 0.83
Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B. ACS Med Chem Lett (2012) 0.83
Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin. ACS Med Chem Lett (2012) 0.83
Interactive effects of competition and predator cues on immune responses of leopard frogs at metamorphosis. J Exp Biol (2013) 0.82
Larval exposure to predator cues alters immune function and response to a fungal pathogen in post-metamorphic wood frogs. Ecol Appl (2013) 0.82
Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes. J Phys Chem B (2013) 0.81
An algorithm for identification and ranking of family-specific residues, applied to the ALDH3 family. Chem Biol Interact (2003) 0.81
MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families. PLoS One (2010) 0.81
Using Caenorhabditis elegans as a model organism for evaluating extracellular signal-regulated kinase docking domain inhibitors. J Cell Commun Signal (2008) 0.81
Hydrophobic residues in small ankyrin 1 participate in binding to obscurin. Mol Membr Biol (2012) 0.80
Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations. J Am Chem Soc (2011) 0.80
Putative irreversible inhibitors of the human sodium-dependent bile acid transporter (hASBT; SLC10A2) support the role of transmembrane domain 7 in substrate binding/translocation. Pharm Res (2012) 0.80
Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations. Chem Biol Interact (2003) 0.80
Strategies for multiple sequence alignment. Biotechniques (2002) 0.79
Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. J Chem Inf Model (2010) 0.79
Computational and experimental characterizations of silver nanoparticle-apolipoprotein biocorona. J Phys Chem B (2013) 0.79
Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach. J Phys Chem Lett (2011) 0.79
Fibrinogen unfolding mechanisms are not too much of a stretch. Structure (2011) 0.79
Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT. J Pharm Sci (2011) 0.78
Comparative studies of vertebrate aldehyde dehydrogenase 3: sequences, structures, phylogeny and evolution. Evidence for a mammalian origin for the ALDH3A1 gene. Chem Biol Interact (2011) 0.78
Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface. J Phys Chem B (2010) 0.78
Prediction of tyrosine sulfation in seven-transmembrane peptide receptors. Endocrine (2002) 0.78
Prediction of tyrosine sulfation sites in animal viruses. Biochem Biophys Res Commun (2003) 0.78
Characterizing structural transitions using localized free energy landscape analysis. PLoS One (2009) 0.77
Inhibition of protein-protein interactions with low molecular weight compounds. Curr Trends Med Chem (2008) 0.77
Mathematically complete nucleotide and protein sequence searching using Ssearch. Curr Protoc Bioinformatics (2004) 0.77
Analysis of single molecule folding studies with replica correlation functions. Chem Phys Lett (2009) 0.77
Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation. J Phys Chem B (2007) 0.76
Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine. Helv Chim Acta (2010) 0.75
Re: Watts et al. Proteins 2002;48:161-168. Proteins (2003) 0.75
Crucial role of position 40 for interactions of CCK-58 revealed by sequence of cat CCK-58. Biochem Biophys Res Commun (2006) 0.75