Published in J Comput Chem on July 23, 2012
The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer (2013) 1.04
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design. Biochim Biophys Acta (2014) 1.01
Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators. Nature (2017) 0.93
Multi-kinase inhibitors can associate with heat shock proteins through their NH2-termini by which they suppress chaperone function. Oncotarget (2016) 0.90
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Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC. Sci Rep (2015) 0.82
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Additive CHARMM force field for naturally occurring modified ribonucleotides. J Comput Chem (2016) 0.79
Iminoguanidines as Allosteric Inhibitors of the Iron-Regulated Heme Oxygenase (HemO) of Pseudomonas aeruginosa. J Med Chem (2016) 0.79
The Role of Cholesterol in Driving IAPP-Membrane Interactions. Biophys J (2016) 0.77
Biologically active LIL proteins built with minimal chemical diversity. Proc Natl Acad Sci U S A (2015) 0.76
Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism. J Physiol (2016) 0.76
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. J Comput Aided Mol Des (2016) 0.76
The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor. Sci Rep (2016) 0.76
Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies. Nucleic Acids Res (2017) 0.75
CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem (2016) 0.75
Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure. Mol Inform (2016) 0.75
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Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur J Med Chem (2016) 0.75
Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem (2016) 0.75
Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine. Int J Mol Sci (2014) 0.75
Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors. Biophys J (2017) 0.75
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Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations. J Chem Theory Comput (2017) 0.75
Testing the ability of rhodanine and 2, 4-thiazolidinedione to interact with the human pancreatic alpha-amylase: electron-density descriptors complement molecular docking, QM, and QM/MM dynamics calculations. J Mol Model (2017) 0.75
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Design, synthesis, and validation of a β-turn mimetic library targeting protein-protein and peptide-receptor interactions. J Am Chem Soc (2011) 0.93
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Conformational and vibrational analysis of methyl methanesulfonate, CH3SO2OCH3. J Phys Chem A (2009) 0.77
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B (2010) 8.70
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B (2005) 3.32
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Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B (2008) 1.57
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
Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran. Biophys J (2007) 1.48
Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction. J Med Chem (2004) 1.41
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J (2002) 1.40
Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comput Sci (2003) 1.37
2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists. J Am Chem Soc (2003) 1.36
Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36
Computational approaches for investigating base flipping in oligonucleotides. Chem Rev (2006) 1.35
Is arginine charged in a membrane? Biophys J (2007) 1.33
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J Comput Chem (2002) 1.32
A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters. Cell Rep (2013) 1.28
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity. J Med Chem (2007) 1.22
Comparison of protein force fields for molecular dynamics simulations. Methods Mol Biol (2008) 1.19
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J Comput Chem (2007) 1.18
All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem (2014) 1.16
A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo. PLoS One (2012) 1.15
Computational identification of inhibitors of protein-protein interactions. Curr Top Med Chem (2007) 1.14
CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B (2010) 1.12
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation. Biophys J (2012) 1.12
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model (2013) 1.09
Divalent metal ion complexes of S100B in the absence and presence of pentamidine. J Mol Biol (2008) 1.09
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model. J Phys Chem B (2010) 1.07
Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. J Med Chem (2004) 1.07
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Res (2003) 1.05
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Proc Natl Acad Sci U S A (2012) 1.05
Atomistic view of base flipping in DNA. Philos Trans A Math Phys Eng Sci (2004) 1.05
The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer (2013) 1.04
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res (2004) 1.03
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem (2011) 1.02
Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol (2009) 1.01
A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. J Phys Chem B (2013) 1.01
Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch. J Mol Biol (2009) 1.01
Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J Mol Biol (2005) 1.00
Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors. Org Biomol Chem (2012) 0.98
Binding response: a descriptor for selecting ligand binding site on protein surfaces. J Chem Inf Model (2007) 0.97
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem (2012) 0.96
Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure. Bioorg Med Chem Lett (2006) 0.95
Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. J Comput Chem (2010) 0.94
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. J Phys Chem B (2014) 0.94
Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations. Biochemistry (2005) 0.93
Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator. J Phys Chem B (2014) 0.93
Regulation of RUNX2 transcription factor-DNA interactions and cell proliferation by vitamin D3 (cholecalciferol) prohormone activity. J Bone Miner Res (2012) 0.91
Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J Phys Chem B (2010) 0.90
Six-site polarizable model of water based on the classical Drude oscillator. J Chem Phys (2013) 0.90
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discuss (2013) 0.90
Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities. ACS Chem Neurosci (2013) 0.90
Position of coordination of the lithium ion determines the regioselectivity of demethylations of 3,4-dimethoxymorphinans with L-selectride. Org Lett (2005) 0.89
Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: novel antimicrobial targets. J Med Chem (2007) 0.89
Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography. Biochemistry (2009) 0.89
Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides. J Phys Chem B (2011) 0.89
Rapid estimation of hydration thermodynamics of macromolecular regions. J Chem Phys (2013) 0.89
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J Comput Aided Mol Des (2014) 0.89
Characterization of ERK docking domain inhibitors that induce apoptosis by targeting Rsk-1 and caspase-9. BMC Cancer (2011) 0.88
Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft. BMC Struct Biol (2007) 0.88
Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations. J Chem Theory Comput (2012) 0.88
Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites. J Am Chem Soc (2010) 0.88
Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments. J Phys Chem B (2014) 0.88
Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties. J Phys Chem Lett (2015) 0.87
Lead validation and SAR development via chemical similarity searching; application to compounds targeting the pY+3 site of the SH2 domain of p56lck. J Chem Inf Model (2005) 0.87
Amphipathic α-helix mimetics based on a 1,2-diphenylacetylene scaffold. Org Lett (2013) 0.87
A search for inhibitors of S100B, a member of the S100 family of calcium-binding proteins. Mini Rev Med Chem (2007) 0.87
Molecular details of the activation of the μ opioid receptor. J Phys Chem B (2013) 0.86
Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase. Proteins (2011) 0.86
Robustness in the fitting of molecular mechanics parameters. J Comput Chem (2015) 0.86
Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J Chem Inf Model (2015) 0.86
Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma. J Clin Invest (2016) 0.86
Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides. J Phys Chem B (2010) 0.85
Intrinsic energy landscapes of amino acid side-chains. J Chem Inf Model (2012) 0.85
Development of extracellular signal-regulated kinase inhibitors. Curr Top Med Chem (2009) 0.84
Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations. Nucleic Acids Res (2005) 0.84
Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model (2015) 0.83
Conformational determinants of the activity of antiproliferative factor glycopeptide. J Chem Inf Model (2013) 0.83
Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives. J Am Chem Soc (2005) 0.83
Functionalization of the 6,14-bridge of the orvinols. 2. Preparation of 18- and 19-hydroxyl-substituted thevinols and their treatment with benzyl bromide. J Org Chem (2005) 0.83
Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore. J Phys Chem B (2011) 0.83
Accurate interaction energies at density functional theory level by means of an efficient dispersion correction. J Chem Phys (2009) 0.83
Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix. J Phys Chem B (2006) 0.83
DNA bending induced by carbocyclic sugar analogs constrained to the north conformation. Biopolymers (2007) 0.82
Small molecule antivirulents targeting the iron-regulated heme oxygenase (HemO) of P. aeruginosa. J Med Chem (2013) 0.82
Small-molecule inhibitors of the ERK signaling pathway: Towards novel anticancer therapeutics. ChemMedChem (2011) 0.82