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Items: 13

1.

Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors.

Granadino-Roldán JM, Mey ASJS, Pérez González JJ, Bosisio S, Rubio-Martinez J, Michel J.

PLoS One. 2019 Mar 12;14(3):e0213217. doi: 10.1371/journal.pone.0213217. eCollection 2019.

2.

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations.

Mey ASJS, Jiménez JJ, Michel J.

J Comput Aided Mol Des. 2018 Jan;32(1):199-210. doi: 10.1007/s10822-017-0083-9. Epub 2017 Nov 13.

3.

Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins.

Schor M, Mey ASJS, MacPhee CE.

Biophys Rev. 2016;8(4):429-439. doi: 10.1007/s12551-016-0234-6. Epub 2016 Nov 22. Review.

4.

Blinded predictions of distribution coefficients in the SAMPL5 challenge.

Bosisio S, Mey AS, Michel J.

J Comput Aided Mol Des. 2016 Nov;30(11):1101-1114. doi: 10.1007/s10822-016-9969-1. Epub 2016 Sep 27.

5.

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.

Bosisio S, Mey ASJS, Michel J.

J Comput Aided Mol Des. 2017 Jan;31(1):61-70. doi: 10.1007/s10822-016-9933-0. Epub 2016 Aug 8.

PMID:
27503495
6.

Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge.

Mey ASJS, Juárez-Jiménez J, Hennessy A, Michel J.

Bioorg Med Chem. 2016 Oct 15;24(20):4890-4899. doi: 10.1016/j.bmc.2016.07.044. Epub 2016 Jul 21.

PMID:
27485604
7.

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study.

Calabrò G, Woods CJ, Powlesland F, Mey AS, Mulholland AJ, Michel J.

J Phys Chem B. 2016 Jun 23;120(24):5340-50. doi: 10.1021/acs.jpcb.6b03296. Epub 2016 Jun 14.

PMID:
27248478
8.

Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models.

Schor M, Mey AS, Noé F, MacPhee CE.

J Phys Chem Lett. 2015 Mar 19;6(6):1076-81. doi: 10.1021/acs.jpclett.5b00330. Epub 2015 Mar 11.

PMID:
26262873
9.

Dynamic properties of force fields.

Vitalini F, Mey AS, Noé F, Keller BG.

J Chem Phys. 2015 Feb 28;142(8):084101. doi: 10.1063/1.4909549.

PMID:
25725706
10.

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.

Wu H, Mey AS, Rosta E, Noé F.

J Chem Phys. 2014 Dec 7;141(21):214106. doi: 10.1063/1.4902240.

PMID:
25481128
11.

Rare-event trajectory ensemble analysis reveals metastable dynamical phases in lattice proteins.

Mey AS, Geissler PL, Garrahan JP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Mar;89(3):032109. Epub 2014 Mar 11.

PMID:
24730792
12.

Variational Approach to Molecular Kinetics.

Nüske F, Keller BG, Pérez-Hernández G, Mey AS, Noé F.

J Chem Theory Comput. 2014 Apr 8;10(4):1739-52. doi: 10.1021/ct4009156. Epub 2014 Mar 6.

PMID:
26580382
13.

EMMA: A Software Package for Markov Model Building and Analysis.

Senne M, Trendelkamp-Schroer B, Mey AS, Schütte C, Noé F.

J Chem Theory Comput. 2012 Jul 10;8(7):2223-38. doi: 10.1021/ct300274u. Epub 2012 Jun 18.

PMID:
26588955

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