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List of works by Alan Mark

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GROMACS: fast, flexible, and free

scientific article (publication date: December 2005)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7

scientific article published on 30 April 2011
An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

scientific article published on 15 November 2011
Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

article
Mechanism of activation of protein kinase JAK2 by the growth hormone receptor

scientific article
Decomposition of the Free Energy of a System in Terms of Specific Interactions

scientific article published on 01 July 1994
Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

scientific article
The Role of histidine residues in low-pH-mediated viral membrane fusion

scientific article published on October 2006
Photoactivation of the photoactive yellow protein: why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein

scientific article published in April 2004
Basic ingredients of free energy calculations: a review

scientific article published on June 2010
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies

scientific article published on 30 January 2014
On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment

scientific article published on 23 November 2009
Calculation of the free energy of solvation for neutral analogs of amino acid side chains

scientific article
Molecular view of hexagonal phase formation in phospholipid membranes

scientific article published on 17 September 2004
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state

scientific article published on 01 September 1992
Histidine protonation and the activation of viral fusion proteins

scientific article
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article
A dynamic pharmacophore drives the interaction between Psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a

scientific article
Ion transport across transmembrane pores

scientific article published on 23 March 2007
Effect of Methyl-Branched Fatty Acids on the Structure of Lipid Bilayers

scientific article published on 19 November 2014
Charge group partitioning in biomolecular simulation

scientific article published on March 2013
The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water

article
Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin

scientific article published on 01 February 2002
Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics

scientific article published on October 18, 2012
The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity

scientific article
The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins

scientific article published on 17 October 2016
Interaction of Tarantula Venom Peptide ProTx-II with Lipid Membranes Is a Prerequisite for Its Inhibition of Human Voltage-gated Sodium Channel NaV1.7.

scientific article published on 16 June 2016
Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore

scientific article
A Ring to Rule Them All: The Effect of Cyclopropane Fatty Acids on the Fluidity of Lipid Bilayers

scientific article published on April 16, 2015
Weak, strong, and coherent regimes of Fröhlich condensation and their applications to terahertz medicine and quantum consciousness

scientific article published on 17 March 2009
Validating lipid force fields against experimental data: Progress, challenges and perspectives.

scientific article
Vancomycin: ligand recognition, dimerization and super-complex formation

scientific article
Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study

article
The Relative Effect of Sterols and Hopanoids on Lipid Bilayers: When Comparable Is Not Identical

scientific article published on 03 December 2013
Missing Fragments: Detecting Cooperative Binding in Fragment-Based Drug Design

scientific article published on February 14, 2012
The Effect of Environment on the Structure of a Membrane Protein: P-Glycoprotein under Physiological Conditions

scientific article published on June 11, 2012
Prediction of the activity and stability effects of site-directed mutagenesis on a protein core

scientific article published on 01 September 1992
On the characterization of host-guest complexes: surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant.

scientific article
Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes.

scientific article
Validation of Molecular Simulation: An Overview of Issues

scientific article
Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible

scientific article (publication date: 13 August 2009)
The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action

scientific article
The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: a molecular dynamics study

scientific article
Developments in Glycopeptide Antibiotics

scientific article
Turning the growth hormone receptor on: evidence that hormone binding induces subunit rotation

scientific article published in April 2010
Calculation of relative free energy via indirect pathways

Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors

scientific article published in July 2011
Structural Characterization of Two Metastable ATP-Bound States of P-Glycoprotein

scientific article published on March 14, 2014
Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a.

scientific article
Deriving Structural Information from Experimentally Measured Data on Biomolecules.

scientific article

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