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List of works by 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

scientific article published on 29 November 2012

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

scientific article

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

scientific article published on 21 February 2014

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

scientific article published on 19 October 2018

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids ⬇️

scientific article published on July 30, 2013

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

scientific article

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

scientific article published on 29 August 2013

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

scientific article

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

scientific article

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

scientific article published in July 2007

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

scientific article published on 6 March 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

scientific article

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

scientific article published on 18 April 2014

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

scientific article published on 13 June 2013

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

scientific article published on 12 January 2017

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

scientific article published on 01 March 2005

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

scientific article published in June 1989

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

scientific article published on 16 November 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. ⬇️

scientific article published on 16 January 2008

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

scientific article published on August 2010

Atomistic view of base flipping in DNA.

scientific article published in July 2004

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

scientific article published on December 6, 2010

Automated conformational energy fitting for force-field development.

scientific article

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

scientific article

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

scientific article published on 28 November 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.

scientific article published on 9 June 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.

scientific article published in January 2006

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

scientific article published on 19 June 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

scientific article published on January 2014

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

scientific article published in November 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

scientific article

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

scientific article published on December 26, 2011

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 24 August 2014

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

scientific article

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

scientific article published on 23 July 2004

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

scientific article published on 26 September 2006

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

scientific article

Characterizing structural transitions using localized free energy landscape analysis

scientific article

Chemical modification of human aldehyde dehydrogenase by physiological substrate

scientific article published on 01 February 1987

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

scientific article published on November 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

scientific article

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

scientific article published on 18 March 2015

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

scientific article published on 10 February 2012

Computational evaluation of protein-small molecule binding.

scientific article published on 21 January 2009

Computational identification of inhibitors of protein-protein interactions.

scientific article published on January 2007

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

scientific article

Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide ⬇️

scientific article published on May 15, 2013

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

scientific article

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

scientific article published on 6 December 2016

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

scientific article

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

scientific article (publication date: 27 January 2011)

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

scientific article

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

scientific article published on February 2015

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

scientific article published in December 2005

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

scientific article published on 12 May 2011

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

scientific article published on 07 August 2020

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

scientific article

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

scientific article published on 02 January 2019

Correction to intrinsic energy landscapes of amino acid side-chains

scientific article published on 18 July 2012

Current status of protein force fields for molecular dynamics simulations

scientific article

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

scientific article published on 20 April 2015

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

scientific article

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

scientific article published on May 11, 2012

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

scientific article published on 11 February 2022

Design of Inhibitors for S100B.

scientific article

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

scientific article published on January 2011

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

scientific article published on January 15, 2012

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

scientific article published on November 2013

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

scientific article published on December 2012

Desmethyl macrolides: synthesis and evaluation of 4-desmethyl telithromycin

scientific article published on 16 July 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.

scientific article

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

scientific article published on December 17, 2010

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

scientific article

Development of extracellular signal-regulated kinase inhibitors.

scientific article published on January 2009

Development of the CHARMM Force Field for Lipids ⬇️

scientific article published on January 1, 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

scientific article published on 26 August 2015

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

scientific article published on 22 December 2014

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

scientific article published on 24 October 2007

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

scientific article published on 23 February 2015

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

scientific article

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

scientific article

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

scientific article published on 21 July 2017

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

scientific article

Empirical force fields for biological macromolecules: overview and issues.

scientific article

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

scientific article

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

scientific article

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

scientific article published on 21 May 2013

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

scientific article published on 10 January 2019

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

scientific article

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

scientific article published on 30 December 2019

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

scientific article published on 4 June 2015

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

scientific article

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

scientific article published in May 2002

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

scientific article published on 30 April 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.

scientific article

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

scientific article published on 06 October 2021

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

scientific article published on August 3, 2011

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

scientific article published on 01 April 2022

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

scientific article

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.

scientific article

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

scientific article published on October 2004

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

scientific article published on October 2000

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

scientific article published on 17 July 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.

scientific article

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

scientific article published on July 2005

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

scientific article

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach ⬇️

scientific article published on June 13, 2013

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

scientific article

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.

scientific article published on 12 February 2013

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

scientific article published on 31 January 2013

Importance of domain closure for the autoactivation of ERK2.

scientific article

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

scientific article published on 13 September 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.

scientific article

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

scientific article

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

scientific article

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

scientific article

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

scientific article

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

scientific article published on August 31, 2011

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

scientific article published in February 2004

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

scientific article

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

scientific article published on 13 April 2015

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

scientific article

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

scientific article published on 05 April 2021

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

scientific article published on 26 July 2021

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

scientific article published on 27 January 2012

Intrinsic energy landscapes of amino acid side-chains.

scientific article published on 24 May 2012

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

scientific article published on August 2013

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

scientific article

Lipopolysaccharide membrane building and simulation.

scientific article

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

scientific article published on 25 February 2015

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

scientific article published on March 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.

scientific article published on 24 June 2013

Molecular dynamics simulations of nucleic acid-protein complexes.

scientific article published on 20 February 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.

scientific article published on 2 May 2008

Molecular modeling and dynamics of neuropeptide Y

article

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

scientific article published in December 2004

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

scientific article

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

scientific article published on January 2006

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

scientific article published on 15 March 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

scientific article published on 10 February 2020

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

scientific article published on January 2012

Optimized Lennard-Jones Parameters for Drug-Like Small Molecules

scientific article

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

scientific article

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

scientific article published on 6 February 2015

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

scientific article published on 04 July 2013

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

scientific article

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.

scientific article published on 22 January 2018

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

scientific article published on 11 April 2017

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

scientific article published on 11 April 2017

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

scientific article published on 17 April 2018

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

scientific article published on October 2013

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

scientific article published on 27 February 2007

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

scientific article

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

scientific article published on September 2009

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

scientific article published on January 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

scientific article published on 06 February 2021

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

scientific article published in January 2002

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

scientific article published on 01 June 2005

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

scientific article published on 25 February 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.

scientific article

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

scientific article published on 17 August 2013

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

scientific article

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

article

Rapid estimation of hydration thermodynamics of macromolecular regions.

scientific article

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

scientific article published in March 2003

Recent Developments and Applications of the CHARMM force fields

scientific article

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

scientific article

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 ⬇️

scientific article published on April 1, 2012

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

scientific article

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

scientific article published on April 25, 2011

Robustness in the fitting of molecular mechanics parameters.

scientific article published on 31 March 2015

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

scientific article published on 6 May 2014

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

scientific article published on 23 February 2021

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

scientific article

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

scientific article published on January 2013

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

scientific article published on January 2015

Six-site polarizable model of water based on the classical Drude oscillator ⬇️

scientific article published on January 21, 2013

Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) ofP. aeruginosa ⬇️

scientific article published on March 14, 2013

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

scientific article

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

scientific article

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

scientific article published on January 3, 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

scientific article

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

scientific article published on 01 January 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.

scientific article

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

scientific article

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

scientific article

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

scientific article published on June 2013

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

scientific article (publication date: 17 June 2013)

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

scientific article published on 01 January 1999

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

scientific article

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

scientific article

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

article

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

scientific article published on February 2010

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

scientific article published on 11 June 2013

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

scientific article

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

scientific article published on 03 July 2013

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

scientific article

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

scientific article published on 12 November 2020

The structure of aqueous guanidinium chloride solutions.

scientific article published in September 2004

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

scientific article published on 12 March 2019

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

scientific article published on 17 September 2013

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

scientific article (publication date: 2013)

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

scientific article

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

scientific article published on 27 February 2008

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

scientific article published on 23 December 2008

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.

scientific article

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

scientific article published on 01 April 1995

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