Published in J Comput Aided Mol Des on June 01, 2004
Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PLoS One (2015) 1.40
Computational studies on the histone deacetylases and the design of selective histone deacetylase inhibitors. Curr Top Med Chem (2009) 0.93
Drug design for ever, from hype to hope. J Comput Aided Mol Des (2012) 0.85
Computational Epigenetics: the new scientific paradigm. Bioinformation (2010) 0.84
Insights from comprehensive multiple receptor docking to HDAC8. J Mol Model (2012) 0.78
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. J Comput Aided Mol Des (2006) 0.77
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61
Translating the histone code. Science (2001) 56.77
Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins (1997) 26.91
Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature (2000) 20.54
Protein structure prediction and structural genomics. Science (2001) 11.76
Modeling of loops in protein structures. Protein Sci (2000) 9.68
Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A. J Biol Chem (1990) 9.21
Histone deacetylases and cancer: causes and therapies. Nat Rev Cancer (2001) 9.12
Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature (1999) 7.47
Histone-deacetylase inhibitors: novel drugs for the treatment of cancer. Nat Rev Drug Discov (2002) 6.97
Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J Biol Chem (2001) 6.85
Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J (2001) 6.85
Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem (1989) 5.23
Recent Advances in Zinc Enzymology. Chem Rev (1996) 4.28
A synthetic inhibitor of histone deacetylase, MS-27-275, with marked in vivo antitumor activity against human tumors. Proc Natl Acad Sci U S A (1999) 3.26
The human histone deacetylase family. Exp Cell Res (2001) 2.86
Apicidin: a novel antiprotozoal agent that inhibits parasite histone deacetylase. Proc Natl Acad Sci U S A (1996) 2.48
Trapoxin, an antitumor cyclic tetrapeptide, is an irreversible inhibitor of mammalian histone deacetylase. J Biol Chem (1993) 2.40
Structure of the histone deacetylase SIRT2. Nat Struct Biol (2001) 2.37
Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (1987) 2.04
FR901228, a potent antitumor antibiotic, is a novel histone deacetylase inhibitor. Exp Cell Res (1998) 1.78
Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins (1995) 1.72
Histone deacetylase inhibitors: from target to clinical trials. Expert Opin Investig Drugs (2002) 1.45
Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation. Biochemistry (2002) 1.27
Psammaplins from the sponge Pseudoceratina purpurea: inhibition of both histone deacetylase and DNA methyltransferase. J Org Chem (2003) 1.25
Inhibitors of human histone deacetylase: synthesis and enzyme and cellular activity of straight chain hydroxamates. J Med Chem (2002) 1.23
Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins (1995) 1.21
Ligand-supported homology modeling of g-protein-coupled receptor sites: models sufficient for successful virtual screening. Angew Chem Int Ed Engl (2004) 1.17
Phosphorus-based SAHA analogues as histone deacetylase inhibitors. Org Lett (2003) 1.04
Development of potential antitumor agents. Synthesis and biological evaluation of a new set of sulfonamide derivatives as histone deacetylase inhibitors. J Med Chem (2003) 1.01
Trifluoromethyl ketones as inhibitors of histone deacetylase. Bioorg Med Chem Lett (2002) 0.99
Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach. J Am Chem Soc (2001) 0.94
Dynamics of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. Biochemistry (2000) 0.92
Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP). Org Biomol Chem (2003) 0.89
Alpha-keto amides as inhibitors of histone deacetylase. Bioorg Med Chem Lett (2003) 0.82
Novel histone deacetylase inhibitors: N-hydroxycarboxamides possessing a terminal bicyclic aryl group. Bioorg Med Chem Lett (2002) 0.82
Role of the flexible loop of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Tritrichomonas foetus in enzyme catalysis. Biochemistry (2001) 0.81
Indole amide hydroxamic acids as potent inhibitors of histone deacetylases. Bioorg Med Chem Lett (2003) 0.75
Thrombin inhibition by novel benzamidine derivatives: a free-energy perturbation study. J Med Chem (2002) 0.75
Critical assessment of the automated AutoDock as a new docking tool for virtual screening. Proteins (2006) 1.21
Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. J Am Chem Soc (2003) 0.92
Freezing transition of interfacial water at room temperature under electric fields. Phys Rev Lett (2005) 0.92
Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc (2005) 0.92
Peptide-cleaving catalyst selective for peptide deformylase. J Am Chem Soc (2005) 0.87
Loop flexibility and solvent dynamics as determinants for the selective inhibition of cyclin-dependent kinase 4: comparative molecular dynamics simulation studies of CDK2 and CDK4. Chembiochem (2004) 0.86
Zwanzig-Mori equation for the time-dependent pair distribution function. Phys Rev E Stat Nonlin Soft Matter Phys (2011) 0.85
Diffusion-influenced reactions involving a reactant with two active sites. J Chem Phys (2009) 0.83
Prediction of the mutation-induced change in thermodynamic stabilities of membrane proteins from free energy simulations. Biophys Chem (2004) 0.80
An efficient molecular dynamics simulation method for calculating the diffusion-influenced reaction rates. J Chem Phys (2004) 0.80
Generalization of Wilemski-Fixman-Weiss decoupling approximation to the case involving multiple sinks of different sizes, shapes, and reactivities. J Chem Phys (2006) 0.79
Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors. J Comput Aided Mol Des (2005) 0.78
Excluded volume effects on the intrachain reaction kinetics. J Phys Chem B (2008) 0.77
Nanosecond molecular dynamics simulations of Cdc25B and its complex with a 1,4-naphthoquinone inhibitor: implications for rational inhibitor design. J Mol Graph Model (2008) 0.77
A rigorous foundation of the diffusion-influenced bimolecular reaction kinetics. J Chem Phys (2009) 0.75
An accurate expression for the rates of diffusion-influenced bimolecular reactions with long-range reactivity. J Chem Phys (2013) 0.75
The optimized Rouse-Zimm theory of excluded volume effects on chain dynamics. J Chem Phys (2004) 0.75
Mean first passage time for the contact between the ends of a chain polymer. J Phys Chem B (2007) 0.75
Kinetics of collision-induced reactions between hard-sphere reactants. J Chem Phys (2009) 0.75
Theory of non-Markovian rate processes. J Phys Chem B (2007) 0.75
Effects of the interaction potential and hydrodynamic interaction on the diffusion-influenced reaction rates. J Chem Phys (2011) 0.75