Works by Mark, Alan E.

Results: 66

Protein α-Turns Recreated in Structurally Stable Small Molecules.

Published in:

Angewandte Chemie, 2011, v. 123, n. 47, p. 11303, doi. 10.1002/ange.201105119

By:

Hoang, Huy N.;
Driver, Russell W.;
Beyer, Renée L.;
Malde, Alpeshkumar K.;
Le, Giang T.;
Abbenante, Giovanni;
Mark, Alan E.;
Fairlie, David P.

Publication type:

Article

Stability of SIV gp32 Fusion-Peptide Single-Layer Protofibrils as Monitored by Molecular-Dynamics Simulations.

Published in:

Angewandte Chemie, 2005, v. 117, n. 7, p. 1089, doi. 10.1002/ange.200461935

By:

Patricia Soto;
Josep Cladera;
Alan E. Mark;
Xavier Daura

Publication type:

Article

Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environment.

Published in:

FEBS Letters, 2020, v. 594, n. 6, p. 1062, doi. 10.1002/1873-3468.13705

By:

Bergen, Glen;
Stroet, Martin;
Caron, Bertrand;
Poger, David;
Mark, Alan E.

Publication type:

Article

Revisiting the scissor-like mechanism of activation for the erythropoietin receptor.

Published in:

FEBS Letters, 2016, v. 590, n. 18, p. 3083, doi. 10.1002/1873-3468.12340

By:

Corbett, Michael S. P.;
Poger, David;
Mark, Alan E.

Publication type:

Article

Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface.

Published in:

Proteins, 2006, v. 64, n. 4, p. 863, doi. 10.1002/prot.20936

By:

Fan, Hao;
Wang, Xiaoqin;
Zhu, Jiang;
Robillard, George T.;
Mark, Alan E.

Publication type:

Article

A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na<sup>+</sup> ions in stabilizing the active site.

Published in:

Proteins, 2005, v. 58, n. 2, p. 450, doi. 10.1002/prot.20304

By:

Kovalskyy, Dmytro;
Dubyna, Volodymyr;
Mark, Alan E.;
Kornelyuk, Alexander

Publication type:

Article

Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study.

Published in:

Proteins, 2003, v. 53, n. 1, p. 111, doi. 10.1002/prot.10496

By:

Hao Fan;
Alan E. Mark

Publication type:

Article

Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes.

Published in:

Proteins, 2002, v. 48, n. 2, p. 212, doi. 10.1002/prot.10135

By:

Groenhof, Gerrit;
Lensink, Marc F.;
Berendsen, Herman J. C.;
Mark, Alan E.

Publication type:

Article

Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore.

Published in:

Proteins, 2002, v. 48, n. 2, p. 202, doi. 10.1002/prot.10136

By:

Groenhof, Gerrit;
Lensink, Marc F.;
Berendsen, Herman J. C.;
Snijders, Jaap G.;
Mark, Alan E.

Publication type:

Article

Folding and stability of the three-stranded β-sheet peptide Betanova: Insights from molecular dynamics simulations.

Published in:

Proteins, 2002, v. 46, n. 4, p. 380, doi. 10.1002/prot.1175

By:

Colombo, Giorgio;
Roccatano, Danilo;
Mark, Alan E.

Publication type:

Article

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

Published in:

Proteins, 2002, v. 46, n. 2, p. 215, doi. 10.1002/prot.1166

By:

Schäfer, Heiko;
Smith, Lorna J.;
Mark, Alan E.;
van Gunsteren, Wilfred F.

Publication type:

Article

Free energy barrier estimation of unfolding the α-helical surfactant-associated polypeptide C.

Published in:

Proteins, 2001, v. 43, n. 4, p. 395, doi. 10.1002/prot.1052

By:

Zangi, Ronen;
Kovacs, Helena;
van Gunsteren, Wilfred F.;
Johansson, Jan;
Mark, Alan E.

Publication type:

Article

Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior.

Published in:

Proteins, 2001, v. 43, n. 1, p. 45, doi. 10.1002/1097-0134(20010401)43:1<45::AID-PROT1016>3.0.CO;2-N

By:

Schäfer, Heiko;
Daura, Xavier;
Mark, Alan E.;
van Gunsteren, Wilfred F.

Publication type:

Article

The effect of motional averaging on the calculation of NMR-derived structural properties.

Published in:

Proteins, 1999, v. 36, n. 4, p. 542, doi. 10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M

By:

Daura, Xavier;
Antes, Iris;
van Gunsteren, Wilfred F.;
Thiel, Walter;
Mark, Alan E.

Publication type:

Article

Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations.

Published in:

Proteins, 1999, v. 34, n. 3, p. 269, doi. 10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO;2-3

By:

Daura, Xavier;
van Gunsteren, Wilfred F.;
Mark, Alan E.

Publication type:

Article

Solvent structure at a hydrophobic protein surface.

Published in:

Proteins, 1997, v. 27, n. 3, p. 395, doi. 10.1002/(SICI)1097-0134(199703)27:3<395::AID-PROT7>3.0.CO;2-C

By:

Kovacs, Helena;
Mark, Alan E.;
van Gunsteren, Wilfred F.

Publication type:

Article

Fundamentals of drug design from a biophysical viewpoint.

Published in:

Quarterly Reviews of Biophysics, 1994, v. 27, n. 4, p. 435, doi. 10.1017/S0033583500003103

By:

Van Gunsteren, Wilfred F.;
King, Paul M.;
Mark, Alan E.

Publication type:

Article

Vancomycin: ligand recognition, dimerization and super-complex formation.

Published in:

FEBS Journal, 2013, v. 280, n. 5, p. 1294, doi. 10.1111/febs.12121

By:

Jia, ZhiGuang;
O'Mara, Megan L.;
Zuegg, Johannes;
Cooper, Matthew A.;
Mark, Alan E.

Publication type:

Article

Does Tautomerization of FapyG Influence Its Mutagenicity?

Published in:

ChemPhysChem, 2014, v. 15, n. 9, p. 1779, doi. 10.1002/cphc.201400045

By:

Jena, Nihar R.;
Mark, Alan E.;
Mishra, Phool C.

Publication type:

Article

On the Relative Merits of Equilibrium and Non-Equilibrium Simulations for the Estimation of Free-Energy Differences.

Published in:

ChemPhysChem, 2010, v. 11, n. 17, p. 3734, doi. 10.1002/cphc.201000562

By:

Daura, Xavier;
Affentranger, Roman;
Mark, Alan E.

Publication type:

Article

Protein α-Turns Recreated in Structurally Stable Small Molecules.

Published in:

Angewandte Chemie International Edition, 2011, v. 50, n. 47, p. 11107, doi. 10.1002/anie.201105119

By:

Hoang, Huy N.;
Driver, Russell W.;
Beyer, Renée L.;
Malde, Alpeshkumar K.;
Le, Giang T.;
Abbenante, Giovanni;
Mark, Alan E.;
Fairlie, David P.

Publication type:

Article

Parametrization of aliphatic CH<sub> n</sub> united atoms of GROMOS96 force field.

Published in:

Journal of Computational Chemistry, 1998, v. 19, n. 5, p. 535, doi. 10.1002/(SICI)1096-987X(19980415)19:5<535::AID-JCC6>3.0.CO;2-N

By:

Daura, Xavier;
Mark, Alan E.;
Van Gunsteren, Wilfred F.

Publication type:

Article

Revealing the Interplay between Charge Transport, Luminescence Efficiency, and Morphology in Organic Light‐Emitting Diode Blends.

Published in:

Advanced Functional Materials, 2020, v. 30, n. 9, p. 1, doi. 10.1002/adfm.201907942

By:

Gao, Mile;
Lee, Thomas;
Burn, Paul L.;
Mark, Alan E.;
Pivrikas, Almantas;
Shaw, Paul E.

Publication type:

Article

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.

Published in:

Journal of Computer-Aided Molecular Design, 2011, v. 25, n. 1, p. 1, doi. 10.1007/s10822-010-9397-6

By:

Malde, Alpeshkumar K.;
Mark, Alan E.

Publication type:

Article

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin.

Published in:

Journal of Computer-Aided Molecular Design, 2003, v. 17, n. 10, p. 673, doi. 10.1023/B:JCAM.0000017374.53591.32

By:

Villa, Alessandra;
Zangi, Ronen;
Pieffet, Gilles;
Mark, Alan E.

Publication type:

Article

Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a.

Published in:

2015

By:

Saez, Natalie J;
Deplazes, Evelyne;
Cristofori ‐ Armstrong, Ben;
Chassagnon, Irène R;
Lin, Xiaozhen;
Mobli, Mehdi;
Mark, Alan E;
Rash, Lachlan D;
King, Glenn F;
Cristofori-Armstrong, Ben;
Chassagnon, Irène R

Publication type:

journal article

The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment.

Published in:

PLoS ONE, 2018, v. 13, n. 1, p. 1, doi. 10.1371/journal.pone.0191882

By:

Condic-Jurkic, Karmen;
Subramanian, Nandhitha;
Mark, Alan E.;
O’Mara, Megan L.

Publication type:

Article

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures.

Published in:

Protein Science: A Publication of the Protein Society, 2006, v. 15, n. 3, p. 441, doi. 10.1110/ps.051721006

By:

Fan, Hao;
Mark, Alan E.

Publication type:

Article

Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures.

Published in:

Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 4, p. 992, doi. 10.1110/ps.03449904

By:

Fan, Hao;
Mark, Alan E.

Publication type:

Article

Refinement of homology-based protein structures by molecular dynamics simulation techniques.

Published in:

Protein Science: A Publication of the Protein Society, 2004, v. 13, n. 1, p. 211, doi. 10.1110/ps.03381404

By:

Fan, Hao;
Mark, Alan E.

Publication type:

Article

On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio‐Molecular Systems: Overview and Perspective on Issues.

Published in:

ChemPhysChem, 2021, v. 22, n. 3, p. 264, doi. 10.1002/cphc.202000968

By:

Gunsteren, Wilfred F.;
Daura, Xavier;
Fuchs, Patrick F. J.;
Hansen, Niels;
Horta, Bruno A. C.;
Hünenberger, Philippe H.;
Mark, Alan E.;
Pechlaner, Maria;
Riniker, Sereina;
Oostenbrink, Chris

Publication type:

Article

Basic ingredients of free energy calculations: A review.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 8, p. 1569, doi. 10.1002/jcc.21450

By:

CHRIST, CLARA D.;
MARK, ALAN E.;
VAN GUNSTEREN, WILFRED F.

Publication type:

Article

A new force field for simulating phosphatidylcholine bilayers.

Published in:

Journal of Computational Chemistry, 2010, v. 31, n. 6, p. 1117, doi. 10.1002/jcc.21396

By:

POGER, DAVID;
VAN GUNSTEREN, WILFRED F.;
MARK, ALAN E.

Publication type:

Article

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 7, p. 1059, doi. 10.1002/jcc.21128

By:

PERIOLE, XAVIER;
ALLEN, LUCY R.;
TAMIOLA, KAMIL;
MARK, ALAN E.;
PACI, EMANUELE

Publication type:

Article

GROMACS: Fast, flexible, and free.

Published in:

Journal of Computational Chemistry, 2005, v. 26, n. 16, p. 1701, doi. 10.1002/jcc.20291

By:

Van Der Spoel, David;
Lindahl, Erik;
Hess, Berk;
Groenhof, Gerrit;
Mark, Alan E.;
Berendsen, Herman J. C.

Publication type:

Article

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.

Published in:

Journal of Computational Chemistry, 2006, v. 27, n. 3, p. 316, doi. 10.1002/jcc.20341

By:

Wassenaar, Tsjerk A.;
Mark, Alan E.

Publication type:

Article

Incorporating the effect of ionic strength in free energy calculations using explicit ions.

Published in:

Journal of Computational Chemistry, 2005, v. 26, n. 2, p. 115, doi. 10.1002/jcc.20156

By:

Donnini, Serena;
Mark, Alan E.;
Juffer, André H.;
Villa, Alessandra

Publication type:

Article

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.

Published in:

Journal of Computational Chemistry, 2004, v. 25, n. 13, p. 1656, doi. 10.1002/jcc.20090

By:

Oostenbrink, Chris;
Villa, Alessandra;
Mark, Alan E.;
Van Gunsteren, Wilfred F.

Publication type:

Article

Calculation of the free energy of solvation for neutral analogs of amino acid side chains.

Published in:

Journal of Computational Chemistry, 2002, v. 23, n. 5, p. 548, doi. 10.1002/jcc.10052

By:

Villa, Alessandra;
Mark, Alan E.

Publication type:

Article

Estimating relative free energies from a single ensemble: Hydration free energies.

Published in:

Journal of Computational Chemistry, 1999, v. 20, n. 15, p. 1604, doi. 10.1002/(SICI)1096-987X(19991130)20:15<1604::AID-JCC2>3.0.CO;2-A

By:

Schäfer, Heiko;
Van Gunsteren, Wilfred F.;
Mark, Alan E.

Publication type:

Article

The recognition of membrane-bound PtdIns3 P by PX domains.

Published in:

Proteins, 2014, v. 82, n. 10, p. 2332, doi. 10.1002/prot.24593

By:

Jia, ZhiGuang;
Ghai, Rajesh;
Collins, Brett M.;
Mark, Alan E.

Publication type:

Article

Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models.

Published in:

Proteins, 2012, v. 80, n. 7, p. 1744, doi. 10.1002/prot.24068

By:

Fan, Hao;
Periole, Xavier;
Mark, Alan E.

Publication type:

Article

Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation.

Published in:

Proteins, 2010, v. 78, n. 5, p. 1163, doi. 10.1002/prot.22636

By:

Poger, David;
Mark, Alan E.

Publication type:

Article

Inclusion of ionization states of ligands in affinity calculations.

Published in:

Proteins, 2009, v. 76, n. 1, p. 138, doi. 10.1002/prot.22326

By:

Donnini, Serena;
Villa, Alessandra;
Groenhof, Gerrit;
Mark, Alan E.;
Wierenga, Rik K.;
Juffer, André H.

Publication type:

Article

Calcium binding to the purple membrane: A molecular dynamics study.

Published in:

Proteins, 2009, v. 74, n. 3, p. 669, doi. 10.1002/prot.22182

By:

Wassenaar, Tsjerk A.;
Daura, Xavier;
Padrós, Esteve;
Mark, Alan E.

Publication type:

Article

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials.

Published in:

Proteins, 2008, v. 72, n. 4, p. 1171, doi. 10.1002/prot.22005

By:

Zhu, Jiang;
Fan, Hao;
Periole, Xavier;
Honig, Barry;
Mark, Alan E.

Publication type:

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.

Published in:

Proteins, 2008, v. 70, n. 2, p. 333, doi. 10.1002/prot.21541

By:

Wassenaar, Tsjerk A.;
Quax, Wim J.;
Mark, Alan E.

Publication type:

Article

Molecular dynamics simulations from putative transition states of α-spectrin SH3 domain.

Published in:

Proteins, 2007, v. 69, n. 3, p. 536, doi. 10.1002/prot.21491

By:

Periole, Xavier;
Vendruscolo, Michele;
Mark, Alan E.

Publication type:

Article

Calculation of the Redox Potential of the Protein Azurin and Some Mutants.

Published in:

ChemBioChem, 2005, v. 6, n. 4, p. 738, doi. 10.1002/cbic.200400244

By:

Marieke van den Bosch;
Marcel Swart;
Jaap G. Snijders†;
Herman J. C. Berendsen;
Alan E. Mark;
Chris Oostenbrink;
Wilfred F. van Gunsteren;
Gerard W. Canters

Publication type:

Article

Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer.

Published in:

Australian Journal of Chemistry, 2014, v. 67, n. 12, p. 1786, doi. 10.1071/CH14396

By:

Casey, Lachlan W.;
Mark, Alan E.;
Kobe, Bostjan

Publication type:

Article