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Items: 24

1.

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.

Elisée E, Gapsys V, Mele N, Chaput L, Selwa E, de Groot BL, Iorga BI.

J Comput Aided Mol Des. 2019 Nov 1. doi: 10.1007/s10822-019-00232-w. [Epub ahead of print]

PMID:
31677003
2.

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches.

Aldeghi M, Gapsys V, de Groot BL.

ACS Cent Sci. 2019 Aug 28;5(8):1468-1474. doi: 10.1021/acscentsci.9b00590. Epub 2019 Aug 13.

3.

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

Gapsys V, de Groot BL.

Elife. 2019 Jun 20;8. pii: e44718. doi: 10.7554/eLife.44718.

4.

Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation.

Coci EG, Gapsys V, Shur N, Shin-Podskarbi Y, de Groot BL, Miller K, Vockley J, Sondheimer N, Ganetzky R, Freisinger P.

Hum Mutat. 2019 Jun;40(6):816-827. doi: 10.1002/humu.23742. Epub 2019 Apr 13.

PMID:
30870574
5.

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation.

Aldeghi M, Gapsys V, de Groot BL.

ACS Cent Sci. 2018 Dec 26;4(12):1708-1718. doi: 10.1021/acscentsci.8b00717. Epub 2018 Dec 13.

6.

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation.

Aldeghi M, de Groot BL, Gapsys V.

Methods Mol Biol. 2019;1851:19-47. doi: 10.1007/978-1-4939-8736-8_2.

PMID:
30298390
7.

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations.

Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV.

J Chem Theory Comput. 2018 Jul 10;14(7):3397-3408. doi: 10.1021/acs.jctc.7b01109. Epub 2018 Jun 21.

PMID:
29847122
8.

Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets.

Sabo TM, Gapsys V, Walter KFA, Fenwick RB, Becker S, Salvatella X, de Groot BL, Lee D, Griesinger C.

Methods. 2018 Apr 1;138-139:85-92. doi: 10.1016/j.ymeth.2018.04.007. Epub 2018 Apr 12.

PMID:
29656081
9.

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.

Gapsys V, de Groot BL.

J Chem Theory Comput. 2017 Dec 12;13(12):6275-6289. doi: 10.1021/acs.jctc.7b00849. Epub 2017 Nov 29.

10.

Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation.

Matthes D, Gapsys V, Griesinger C, de Groot BL.

ACS Chem Neurosci. 2017 Dec 20;8(12):2791-2808. doi: 10.1021/acschemneuro.7b00325. Epub 2017 Sep 28.

11.

pmx Webserver: A User Friendly Interface for Alchemistry.

Gapsys V, de Groot BL.

J Chem Inf Model. 2017 Feb 27;57(2):109-114. doi: 10.1021/acs.jcim.6b00498. Epub 2017 Feb 16.

PMID:
28181802
12.

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.

Matthes D, Gapsys V, Brennecke JT, de Groot BL.

Sci Rep. 2016 Sep 12;6:33156. doi: 10.1038/srep33156.

13.

Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.

Ilgü H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, Fotiadis D.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10358-63. doi: 10.1073/pnas.1605442113. Epub 2016 Aug 31.

14.

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan.

Gapsys V, Michielssens S, Seeliger D, de Groot BL.

Angew Chem Int Ed Engl. 2016 Jun 20;55(26):7364-8. doi: 10.1002/anie.201510054. Epub 2016 Apr 28.

15.

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

Rauscher S, Gapsys V, Gajda MJ, Zweckstetter M, de Groot BL, Grubmüller H.

J Chem Theory Comput. 2015 Nov 10;11(11):5513-24. doi: 10.1021/acs.jctc.5b00736. Epub 2015 Oct 22.

PMID:
26574339
16.

Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings.

Gapsys V, Narayanan RL, Xiang S, de Groot BL, Zweckstetter M.

J Biomol NMR. 2015 Nov;63(3):299-307. doi: 10.1007/s10858-015-9990-z. Epub 2015 Oct 3.

PMID:
26433382
17.

pmx: Automated protein structure and topology generation for alchemical perturbations.

Gapsys V, Michielssens S, Seeliger D, de Groot BL.

J Comput Chem. 2015 Feb 15;36(5):348-54. doi: 10.1002/jcc.23804. Epub 2014 Dec 8.

18.

Calculation of binding free energies.

Gapsys V, Michielssens S, Peters JH, de Groot BL, Leonov H.

Methods Mol Biol. 2015;1215:173-209. doi: 10.1007/978-1-4939-1465-4_9.

PMID:
25330964
19.

Phosphorylation drives a dynamic switch in serine/arginine-rich proteins.

Xiang S, Gapsys V, Kim HY, Bessonov S, Hsiao HH, Möhlmann S, Klaukien V, Ficner R, Becker S, Urlaub H, Lührmann R, de Groot B, Zweckstetter M.

Structure. 2013 Dec 3;21(12):2162-74. doi: 10.1016/j.str.2013.09.014. Epub 2013 Oct 31.

20.

Computational analysis of local membrane properties.

Gapsys V, de Groot BL, Briones R.

J Comput Aided Mol Des. 2013 Oct;27(10):845-58. doi: 10.1007/s10822-013-9684-0. Epub 2013 Oct 23.

21.

Optimal superpositioning of flexible molecule ensembles.

Gapsys V, de Groot BL.

Biophys J. 2013 Jan 8;104(1):196-207. doi: 10.1016/j.bpj.2012.11.003. Epub 2013 Jan 8.

22.

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

Gapsys V, Seeliger D, de Groot BL.

J Chem Theory Comput. 2012 Jul 10;8(7):2373-82. doi: 10.1021/ct300220p. Epub 2012 Jun 6.

PMID:
26588970
23.

Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations.

Matthes D, Gapsys V, de Groot BL.

J Mol Biol. 2012 Aug 10;421(2-3):390-416. doi: 10.1016/j.jmb.2012.02.004. Epub 2012 Feb 8.

24.

Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization.

Matthes D, Gapsys V, Daebel V, de Groot BL.

PLoS One. 2011 May 3;6(5):e19129. doi: 10.1371/journal.pone.0019129.

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