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Items: 28

1.

Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression.

Bastolla U, Dehouck Y.

J Chem Inf Model. 2019 Oct 29. doi: 10.1021/acs.jcim.9b00627. [Epub ahead of print]

PMID:
31600071
2.

The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models.

Dehouck Y, Bastolla U.

Integr Biol (Camb). 2017 Jul 17;9(7):627-641. doi: 10.1039/c7ib00079k.

PMID:
28555214
3.

Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.

de la Higuera I, Ferrer-Orta C, de Ávila AI, Perales C, Sierra M, Singh K, Sarafianos SG, Dehouck Y, Bastolla U, Verdaguer N, Domingo E.

Genome Biol Evol. 2017 May 1;9(5):1212-1228. doi: 10.1093/gbe/evx075.

4.

What evolution tells us about protein physics, and protein physics tells us about evolution.

Bastolla U, Dehouck Y, Echave J.

Curr Opin Struct Biol. 2017 Feb;42:59-66. doi: 10.1016/j.sbi.2016.10.020. Epub 2016 Nov 16. Review.

PMID:
27865208
5.

Protein thermostability prediction within homologous families using temperature-dependent statistical potentials.

Pucci F, Dhanani M, Dehouck Y, Rooman M.

PLoS One. 2014 Mar 19;9(3):e91659. doi: 10.1371/journal.pone.0091659. eCollection 2014.

6.

Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics.

Dehouck Y, Mikhailov AS.

PLoS Comput Biol. 2013;9(8):e1003209. doi: 10.1371/journal.pcbi.1003209. Epub 2013 Aug 29.

7.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

8.

BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.

Dehouck Y, Kwasigroch JM, Rooman M, Gilis D.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. doi: 10.1093/nar/gkt450. Epub 2013 May 30.

9.

Structure-based mutant stability predictions on proteins of unknown structure.

Gonnelli G, Rooman M, Dehouck Y.

J Biotechnol. 2012 Oct 31;161(3):287-93. doi: 10.1016/j.jbiotec.2012.06.020. Epub 2012 Jul 8.

PMID:
22782143
10.

Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data.

Rooman M, Albert J, Dehouck Y, Haye A.

PLoS One. 2011;6(12):e27948. doi: 10.1371/journal.pone.0027948. Epub 2011 Dec 15.

11.

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site.

Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N.

Bioinformatics. 2011 Dec 1;27(23):3286-92. doi: 10.1093/bioinformatics/btr576. Epub 2011 Oct 13.

12.

Flanking domain stability modulates the aggregation kinetics of a polyglutamine disease protein.

Saunders HM, Gilis D, Rooman M, Dehouck Y, Robertson AL, Bottomley SP.

Protein Sci. 2011 Oct;20(10):1675-81. doi: 10.1002/pro.698. Epub 2011 Aug 18.

13.

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

Dehouck Y, Kwasigroch JM, Gilis D, Rooman M.

BMC Bioinformatics. 2011 May 13;12:151. doi: 10.1186/1471-2105-12-151.

14.

Evidence that interaction between conserved residues in transmembrane helices 2, 3, and 7 are crucial for human VPAC1 receptor activation.

Chugunov AO, Simms J, Poyner DR, Dehouck Y, Rooman M, Gilis D, Langer I.

Mol Pharmacol. 2010 Sep;78(3):394-401. doi: 10.1124/mol.110.063578. Epub 2010 Jun 23.

PMID:
20573782
15.

Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials.

Folch B, Dehouck Y, Rooman M.

Biophys J. 2010 Feb 17;98(4):667-77. doi: 10.1016/j.bpj.2009.10.050.

16.

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.

Dehouck Y, Grosfils A, Folch B, Gilis D, Bogaerts P, Rooman M.

Bioinformatics. 2009 Oct 1;25(19):2537-43. doi: 10.1093/bioinformatics/btp445. Epub 2009 Aug 3.

PMID:
19654118
17.

Modeling the temporal evolution of the Drosophila gene expression from DNA microarray time series.

Haye A, Dehouck Y, Kwasigroch JM, Bogaerts P, Rooman M.

Phys Biol. 2009 Jan 27;6(1):016004. doi: 10.1088/1478-3975/6/1/016004.

PMID:
19171963
18.

Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity.

Dehouck Y, Folch B, Rooman M.

Protein Eng Des Sel. 2008 Apr;21(4):275-8. doi: 10.1093/protein/gzn001. Epub 2008 Feb 2.

PMID:
18245807
19.

Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials.

Folch B, Rooman M, Dehouck Y.

J Chem Inf Model. 2008 Jan;48(1):119-27. Epub 2007 Dec 28.

PMID:
18161956
20.

Enhancing the stability and solubility of TEV protease using in silico design.

Cabrita LD, Gilis D, Robertson AL, Dehouck Y, Rooman M, Bottomley SP.

Protein Sci. 2007 Nov;16(11):2360-7. Epub 2007 Sep 28.

21.
22.

A new generation of statistical potentials for proteins.

Dehouck Y, Gilis D, Rooman M.

Biophys J. 2006 Jun 1;90(11):4010-7. Epub 2006 Mar 13.

23.
24.

Sequence-structure signals of 3D domain swapping in proteins.

Dehouck Y, Biot C, Gilis D, Kwasigroch JM, Rooman M.

J Mol Biol. 2003 Jul 25;330(5):1215-25.

PMID:
12860140
25.

In vitro and in silico design of alpha1-antitrypsin mutants with different conformational stabilities.

Gilis D, McLennan HR, Dehouck Y, Cabrita LD, Rooman M, Bottomley SP.

J Mol Biol. 2003 Jan 17;325(3):581-9.

PMID:
12498804
26.

PoPMuSiC, rationally designing point mutations in protein structures.

Kwasigroch JM, Gilis D, Dehouck Y, Rooman M.

Bioinformatics. 2002 Dec;18(12):1701-2.

PMID:
12490462
27.

What is paradoxical about Levinthal paradox?

Rooman M, Dehouck Y, Kwasigroch JM, Biot C, Gilis D.

J Biomol Struct Dyn. 2002 Dec;20(3):327-9.

PMID:
12437370
28.

Probing proteins in solution by (129)Xe NMR spectroscopy.

Locci E, Dehouck Y, Casu M, Saba G, Lai A, Luhmer M, Reisse J, Bartik K.

J Magn Reson. 2001 Jun;150(2):167-74.

PMID:
11384176

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