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Lista de obras de Alex MacKerell

(Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters

artículo científico publicado en 2012

2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists.

artículo científico publicado en 2003

A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers

artículo científico publicado en 2014

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

artículo científico publicado en 2018

A Small-Molecule Inhibitor of BCL6 Kills DLBCL Cells In Vitro and In Vivo

artículo científico publicado en 2010

A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.

artículo científico publicado en 2013

A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells.

artículo científico publicado en 2015

A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo.

artículo científico publicado en 2012

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

artículo científico publicado en 2007

Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5

artículo científico publicado en 2015

Additive CHARMM36 Force Field for Nonstandard Amino Acids

scientific article published on 19 May 2021

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers

scientific article published on 01 May 2007

Additive empirical force field for hexopyranose monosaccharides

artículo científico publicado en 2008

All-atom polarizable force field for DNA based on the classical Drude oscillator model

artículo científico publicado en 2014

Amphipathic α-helix mimetics based on a 1,2-diphenylacetylene scaffold.

artículo científico publicado en 2013

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

artículo científico publicado en 2017

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer

artículo científico publicado en 2005

Analysis of structure-function relationships of neuropeptide Y using molecular dynamics simulations and pharmacological activity and binding measurements.

artículo científico publicado en 1989

Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations

artículo científico publicado en 2020

Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator

article

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study. ⬇️

artículo científico publicado en 2008

Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface.

artículo científico publicado en 2010

Atomistic view of base flipping in DNA.

artículo científico publicado en 2004

Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness ⬇️

artículo científico publicado el 6 de diciembre de 2010

Automated conformational energy fitting for force-field development.

artículo científico publicado en 2008

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

artículo científico publicado en 2012

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

artículo científico publicado en 2012

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

scientific article published on 24 May 2020

Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

artículo científico publicado en 2014

Base Flipping in a GCGC Containing DNA Dodecamer:  A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

artículo científico publicado en 2006

Bifurcated hydrogen bonding and asymmetric fluctuations in a carbohydrate crystal studied via X-ray crystallography and computational analysis.

artículo científico publicado en 2013

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

article

Boc-protected 1-(3-oxocycloalkyl)ureas via a one-step Curtius rearrangement: mechanism and scope

artículo científico publicado en 2014

CH/pi interactions involving aromatic amino acids: refinement of the CHARMM tryptophan force field.

artículo científico publicado en 2005

CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol

scientific article published on 01 November 2008

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

artículo científico publicado en 2009

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates ⬇️

artículo científico publicado el 26 de diciembre de 2011

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

artículo científico publicado en 2015

CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.

artículo científico publicado en 2018

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

artículo científico publicado en 2009

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

artículo científico publicado en 2011

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

artículo científico publicado en 2010

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

artículo científico publicado en 2014

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

artículo científico publicado en 2014

CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

artículo científico publicado en 2004

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

artículo científico publicado en 2007

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

artículo científico publicado en 2010

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

artículo científico publicado en 2014

CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data

artículo científico publicado en 2013

Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field

scientific article published on 28 December 2018

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase

artículo científico publicado en 2004

Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure

artículo científico publicado en 2006

Characterization of ERK docking domain inhibitors that induce apoptosis by targeting Rsk-1 and caspase-9.

artículo científico publicado en 2011

Characterizing structural transitions using localized free energy landscape analysis

artículo científico publicado en 2009

Chemical modification of human aldehyde dehydrogenase by physiological substrate

artículo científico publicado en 1987

Chemical substituent effect on pyridine permeability and mechanistic insight from computational molecular descriptors.

artículo científico publicado en 2006

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg

scientific article published on 18 July 2018

Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling

artículo científico publicado en 2010

Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.

artículo científico publicado en 2015

Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.

artículo científico publicado en 2012

Computational evaluation of protein-small molecule binding.

artículo científico publicado en 2009

Computational identification of inhibitors of protein-protein interactions.

artículo científico publicado en 2007

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

artículo científico publicado en 2011

Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

artículo científico publicado en 2015

Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4.

artículo científico publicado en 2016

Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

artículo científico publicado en 2005

Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides

artículo científico publicado en 2011

Conformational properties of α- or β-(1→6)-linked oligosaccharides: Hamiltonian replica exchange MD simulations and NMR experiments

artículo científico publicado en 2014

Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).

artículo científico publicado en 2015

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

artículo científico publicado en 2005

Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore.

artículo científico publicado en 2011

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister Ribozyme

artículo científico publicado en 2020

Cooperative binding of DNA and CBFbeta to the Runt domain of the CBFalpha studied via MD simulations.

artículo científico publicado en 2005

Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg"

artículo científico publicado en 2019

Correction to intrinsic energy landscapes of amino acid side-chains

artículo científico publicado en 2012

Current status of protein force fields for molecular dynamics simulations

artículo científico publicado en 2015

Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5.

artículo científico publicado en 2015

Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs.

artículo científico publicado en 2011

Deconstructing 14-phenylpropyloxymetopon: Minimal requirements for binding to mu opioid receptors ⬇️

artículo científico publicado el 11 de mayo de 2012

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field

artículo científico publicado en 2022

Design of Inhibitors for S100B.

artículo científico publicado en 2005

Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin.

artículo científico publicado en 2011

Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin ⬇️

artículo científico publicado el 15 de enero de 2012

Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin.

artículo científico publicado en 2013

Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin

artículo científico publicado en 2012

Desmethyl macrolides: synthesis and evaluation of 4-desmethyl telithromycin

artículo científico publicado en 2014

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

scientific article published on 01 January 2005

Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water

article

Development and current status of the CHARMM force field for nucleic acids.

artículo científico publicado en 2000

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model ⬇️

artículo científico publicado el 17 de diciembre de 2010

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

artículo científico publicado en 2007

Development of extracellular signal-regulated kinase inhibitors.

scientific article published on January 2009

Development of the CHARMM Force Field for Lipids ⬇️

artículo científico publicado el 1 de enero de 2011

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding

artículo científico publicado en 2015

Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties.

artículo científico publicado en 2014

Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation.

artículo científico publicado en 2007

Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution.

artículo científico publicado en 2015

Divalent Metal Ion Complexes of S100B in the Absence and Presence of Pentamidine

artículo científico publicado en 2008

Do Halogen-Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand-Protein Binding?

artículo científico publicado en 2017

Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives

scientific article published on 29 August 2019

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

artículo científico

Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies.

artículo científico publicado en 2011

Empirical force fields for biological macromolecules: overview and issues.

artículo científico publicado en 2004

Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.

artículo científico publicado en 2015

Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction

artículo científico publicado en 2016

Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations.

artículo científico publicado en 2013

Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology

artículo científico publicado en 2019

Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

artículo científico publicado en 2012

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

artículo científico publicado en 2019

Facile Synthesis of Spirocyclic Lactams from β-Keto Carboxylic Acids.

artículo científico publicado en 2015

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

artículo científico publicado en 2013

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

artículo científico publicado en 2002

Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation

artículo científico publicado en 2021

Functionalization of the 6,14-bridge of the orvinols. 2. Preparation of 18- and 19-hydroxyl-substituted thevinols and their treatment with benzyl bromide.

artículo científico publicado en 2005

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field

artículo científico publicado en 2021

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins ⬇️

artículo científico publicado el 3 de agosto de 2011

Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field

artículo científico publicado en 2022

Holo-Ni(II) Hp NikR Is an Asymmetric Tetramer Containing Two Different Nickel-Binding Sites

artículo científico publicado en 2010

Human mitochondrial aldehyde dehydrogenase inhibition by diethyldithiocarbamic acid methanethiol mixed disulfide: a derivative of disulfiram

article

Hydrophobic residues in small ankyrin 1 participate in binding to obscurin.

artículo científico publicado en 2012

Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

artículo científico publicado en 2004

Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets.

artículo científico publicado en 2000

Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design

artículo científico publicado en 2018

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.

artículo científico publicado en 2004

Identification of novel extracellular signal-regulated kinase docking domain inhibitors.

artículo científico publicado en 2005

Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT.

artículo científico publicado en 2011

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

artículo científico publicado en 2011

Impact of electronic polarizability on protein-functional group interactions

scientific article published on 01 April 2020

Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.

artículo científico publicado en 2013

Impact of substrate protonation and tautomerization states on interactions with the active site of arginase I.

artículo científico publicado en 2013

Importance of domain closure for the autoactivation of ERK2.

artículo científico publicado en 2011

Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins

artículo científico publicado en 2019

Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields

scientific article published on 27 November 2018

Improved treatment of the protein backbone in empirical force fields.

artículo científico publicado en 2004

Inactivation of lactate dehydrogenase by UV radiation in the 300 nm wavelength region

article

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

artículo científico publicado en 2012

Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach

artículo científico publicado en 2013

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

artículo científico publicado en 2014

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide

artículo científico publicado en 2014

Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides ⬇️

artículo científico publicado el 31 de agosto de 2011

Influence of conformation on the EPR spectrum of 5,5-dimethyl-1-hydroperoxy-1-pyrrolidinyloxyl: a spin trapped adduct of superoxide.

artículo científico publicado en 2004

Inhibition of (cytosine C5)-methyltransferase by oligonucleotides containing flexible (cyclopentane) and conformationally constrained (bicyclo[3.1.0]hexane) abasic sites.

artículo científico publicado en 2001

Inhibition of TLR2 signaling by small molecule inhibitors targeting a pocket within the TLR2 TIR domain

artículo científico publicado en 2015

Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: novel antimicrobial targets.

artículo científico publicado en 2007

Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A

artículo científico publicado en 2021

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

artículo científico publicado en 2021

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

artículo científico publicado en 2012

Intrinsic energy landscapes of amino acid side-chains.

artículo científico publicado en 2012

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

artículo científico publicado en 2013

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

artículo científico publicado en 2012

Lipopolysaccharide membrane building and simulation.

artículo científico publicado en 2015

Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors

artículo científico publicado en 2015

Mitogen activated protein (MAP) kinases: development of ATP and non-ATP dependent inhibitors.

artículo científico publicado en 2006

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

scientific article published on 29 May 2019

Molecular details of the activation of the μ opioid receptor.

artículo científico publicado en 2013

Molecular dynamics simulations of nucleic acid-protein complexes.

artículo científico publicado en 2008

Molecular dynamics simulations of ribonuclease T1

scientific article published on 01 January 1988

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

article

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

artículo científico publicado en 2008

Molecular modeling and dynamics of neuropeptide Y

article

Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation.

artículo científico publicado en 2004

Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter.

artículo científico publicado en 2010

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

artículo científico publicado en 2006

Novel Noncatalytic Substrate-Selective p38α-Specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-Inflammatory Activity.

artículo científico publicado en 2017

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization

scientific article published on 08 May 2019

Optimization of a Benzothiazole Indolene Scaffold Targeting Bacterial Cell Wall Assembly

artículo científico publicado en 2020

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

artículo científico publicado en 2012

Optimized Lennard-Jones Parameters for Drug-Like Small Molecules.

artículo científico publicado en 2018

Perturbation of long-range water dynamics as the mechanism for the antifreeze activity of antifreeze glycoprotein.

artículo científico publicado en 2014

Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules.

artículo científico publicado en 2015

Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies

artículo científico publicado en 2013

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

artículo científico publicado en 2009

Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model

article

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

artículo científico publicado en 2018

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

artículo científico publicado en 2017

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

artículo científico publicado en 2017

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

artículo científico publicado en 2018

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

artículo científico publicado en 2013

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

artículo científico publicado en 2007

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

artículo científico publicado en 2014

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator.

artículo científico publicado en 2009

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

artículo científico publicado en 2007

Polarizable force field for RNA based on the classical drude oscillator

scientific article published on 01 December 2018

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

artículo científico publicado en 2021

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

artículo científico publicado en 2002

Position of Coordination of the Lithium Ion Determines the Regioselectivity of Demethylations of 3,4-Dimethoxymorphinans with L-Selectride

artículo científico publicado en 2005

Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES-Fatty Acid Micellar System

artículo científico publicado en 2020

Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning

scientific article published on 27 December 2018

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

scientific article published on April 1996

Protein dynamics

article

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

artículo científico publicado en 2002

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure

artículo científico publicado en 2013

Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor.

artículo científico publicado en 2015

Quantum Mechanical Analysis of 1,2-Ethanediol Conformational Energetics and Hydrogen Bonding

article

Rapid estimation of hydration thermodynamics of macromolecular regions.

artículo científico publicado en 2013

Rearrangement of 5-trimethylsilylthebaine on treatment with L-selectride: an efficient synthesis of (+)-bractazonine.

artículo científico publicado en 2003

Recent Developments and Applications of the CHARMM force fields

artículo científico publicado en 2012

Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach.

artículo científico publicado en 2011

Reevaluation of Stereoelectronic Contributions to the Conformational Properties of the Phosphodiester and N3‘-Phosphoramidate Moieties of Nucleic Acids

scientific article published on 01 July 2001

Regulation of RUNX2 transcription factor–DNA interactions and cell proliferation by vitamin D3 (cholecalciferol) prohormone activity ⬇️

artículo científico publicado el 1 de abril de 2012

Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors.

artículo científico publicado en 2012

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations ⬇️

artículo científico publicado el 25 de abril de 2011

Robustness in the fitting of molecular mechanics parameters.

artículo científico publicado en 2015

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

artículo científico publicado en 2014

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion

artículo científico publicado en 2021

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

artículo científico publicado en 2010

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

artículo científico publicado en 2013

Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design

artículo científico publicado en 2015

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

artículo científico publicado en 2009

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf

artículo científico publicado en 2015

Small‐Molecule Inhibitors of the ERK Signaling Pathway: Towards Novel Anticancer Therapeutics ⬇️

artículo científico publicado el 3 de enero de 2011

Solvation dynamics: improved reproduction of the time-dependent Stokes shift with polarizable empirical force field chromophore models

scientific article published on 01 August 2019

Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability

artículo científico publicado en 2015

Specificity in Protein–DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI

artículo científico publicado en 2005

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

scientific article published on 01 September 2020

Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence.

artículo científico publicado en 2013

Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates.

artículo científico publicado en 2010

Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase.

artículo científico publicado en 2011

Structural modifications of (Z)-3-(2-aminoethyl)-5-(4-ethoxybenzylidene)thiazolidine-2,4-dione that improve selectivity for inhibiting the proliferation of melanoma cells containing active ERK signaling

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Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis

artículo científico publicado en 2013

Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads

artículo científico publicado en 1999

Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B

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Structure-activity exploration of a small-molecule Lipid II inhibitor

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Surface-induced alteration of adsorbate electronic structure and intramolecular vibrational coupling: The vibrational spectrum of 2-propoxide on Mo(110) as determined by ab initio calculations and experiments

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Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine.

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Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities.

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Targeting NAD Biosynthesis in Bacterial Pathogens: Structure-Based Development of Inhibitors of Nicotinate Mononucleotide Adenylyltransferase NadD

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Targeting protein tyrosine phosphatase SHP2 for the treatment of PTPN11-associated malignancies

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Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade.

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The SKI complex is a broad-spectrum, host-directed antiviral drug target for coronaviruses, influenza, and filoviruses

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The structure of aqueous guanidinium chloride solutions.

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Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization

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Transmembrane domain II of the human bile acid transporter SLC10A2 coordinates sodium translocation

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Turning defense into offense: defensin mimetics as novel antibiotics targeting lipid II

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Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.

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Understanding the dielectric properties of liquid amides from a polarizable force field.

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Using Caenorhabditis elegans as a model organism for evaluating extracellular signal-regulated kinase docking domain inhibitors

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Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale:  Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding Link Module of TSG-6.

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pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis

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