Biologia Computacional

(Unitat: Proteňmica Aplicada i Enginyeria de Proteďnes)

 

Coordinador

Xavier Daura
Professor d'Investigació ICREA
(www.icrea.cat)
Professor Associat Dept. Bioquímica i Biologia Molecular
Tel. despatx: (+34)935 86 89 40
Tel. laboratori: (+34)935 86 89 39
Fax: (+34)935 81 20 11
E-mail: Xavier.Daura@uab.cat

 

Linies de Recerca

El principal objectiu del nostre grup de recerca és el desenvolupament de noves estratègies per combatre les infeccions per bacteris resistents a múltiples fàrmacs (MDR), en particular, del grup dels gram negatius (GN). La creixent aparició i propagació de patògens resistents a múltiples fàrmacs constitueix en l'actualitat una de les principals amenaces per a la salut pública en tot el món. L'escassetat d'antimicrobians efectius per al tractament de les infeccions per bacteris gram-negatius multiresistents és particularment crítica, donat el nombre creixent de casos de pan-resistència (i.e. a tots els fàrmacs). Per tant, el descobriment de noves dianes farmacològiques i modes d'acció (MoA), menys propicis a l'aparició de resistències, s'ha convertit en una necessitat urgent. Alhora, s'espera que el desenvolupament de vacunes efectives pugui oferir una solució per als grups de població d'alt risc. El nostre equip combina una varietat de tècniques computacionals i experimentals per a la identificació de candidats antigènics per a vacunes i dianes antimicrobianes amb nous modes d'acció en bacteris gram negatius. Gran part d'aquesta investigació es realitza en col·laboració amb el grup de Genètica Molecular Bacteriana de l'IBB, dirigit per Isidre Gibert. En el vessant antimicrobià, el nostre objectiu és explotar factors de virulència conservats com a noves dianes farmacològiques, reduint d'aquesta manera la capacitat patogènica dels bacteris així com la pressió selectiva sobre fenotips resistents als fàrmacs i prevenint l'efecte devastador del tractament amb antibiòtics sobre la microbiota del pacient. En aquestes àrees el nostre grup ha coordinat dos projectes europeus dins del FP6 (BacAbs, identificació de nous antígens) i FP7 (AntiPathoGN, identificació de noves dianes i antibacterians).

Específicament, desenvolupem els següents tipus d'activitats:

 

Eines Bioinformàtiques

 

 

Cap de Grup:

Daura Ribera, Xavier

Membres:

 

 

Research articles and reviews in WoS-indexed journals

2016

[96] E. Scholz, A. Mestre-Ferrer, X. Daura, N. García-Medel, M. Carrascal, E. A. James, W. W. Kwok, F. Canals, I. Alvarez.
A comparative analysis of the peptide repertoires of HLA-DR molecules differentially associated to rheumatoid arthritis.
Arthritis Rheumatol. 2016, in press

[95] M. Ferrer-Navarro, G. Torrent, E. Mongiardini, O. Conchillo-Solé, Isidre Gibert, X. Daura.
Proteomic analysis of outer membrane proteins and vesicles of a clinical isolate and a collection strain of Stenotrophomonas maltophilia.
J. Proteomics 2016, 142: 122-129

[94] D. Petrov, X. Daura, B. Zagrovic.
Effect of oxidative damage on the stability and dimerization of superoxide dismutase 1.
Biophys. J. 2016, 110(7): 1499-1509

[93] M. Pesarrodona, Y. Fernández, L. Foradada, A. Sánchez-Chardi, O. Conchillo-Solé, U. Unzueta, Z. Xu, M. Roldán, S. Villegas, N. Ferrer-Miralles, S. Schwartz, U. Rinas, X. Daura, I. Abasolo, E. Vázquez, A. Villaverde.
Conformational and functional variants of CD44-targeted protein nanoparticles bio-produced in bacteria.
Biofabrication 2016, 8(2): 025001

2015

[92] F. Rueda, M. V. Céspedes, O. Conchillo-Solé, A. Sanchez-Chardi, J. Seras-Franzoso, R. Cubarsi, A. Gallardo, M. Pesarrodona, N. Ferrer-Miralles, X. Daura, E. Vázquez, E. García-Fruitós, R. Mangues, U. Unzueta, A. Villaverde.
Bottom-Up Instructive Quality Control in the Biofabrication of Smart Protein Materials.
Adv. Mater. 2015, 27(47): 7816-7822

[91] P. Huedo, D. Yero, S. Martínez-Servat, A. Ruyra, N. Roher, X. Daura, I. Gibert.
Decoding the genetic and functional diversity of the DSF Quorum-Sensing system in Stenotrophomonas maltophilia.
Front. Microbiol. 2015, 6: 761

[90] R. Zambrano, O. Conchillo-Sole, V. Iglesias, R. Illa, F. Rousseau, J. Schymkowitz, R. Sabate, X. Daura, S. Ventura.
PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores.
Nucleic Acids Res. 2015, 43: W331-W337

[89] A. Nithichanon, D. Rinchai, A. Gori, P. Lassaux, C. Peri, O. Conchillio-Solé, M. Ferrer-Navarro, L. Gourlay, M. Nardini, J. Vila, X. Daura, G. Colombo, M. Bolognesi, G. Lertmemongkolchai.
Sequence- and Structure-based immunoreactive epitope discovery for Burkholderia pseudomallei flagellin.
PLoS Negl. Trop. Dis. 2015, 9(7): e0003917

[88] P. Martínez, P. Huedo, S. Martínez-Servat, R. Planell, M. Ferrer-Navarro, X. Daura, D. Yero, I. Gibert.
Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839).
Front. Cell. Infect. Microbiol. 2015, 5: 41

[87] L. Gourlay, R. Thomas, C. Peri, O. Conchillo Solé, M. Ferrer-Navarro, A. Nithichanon, J. Vila, X. Daura, G. Lertmemongkolchai, R. Titball, G. Colombo, M. Bolognesi.
From crystal structure to in silico epitope discovery in Burkholderia pseudomallei flagellar hook-associated protein FlgK.
FEBS J. 2015, 282(7): 1319-1333

[86] D. Gaudesi, C. Peri, G. Quilici, A. Gori, M. Ferrer-Navarro, O. Conchillo-Solé, R. Thomas, A. Nithichanon, G. Lertmemongkolchai, R. Titball, X. Daura, G. Colombo, G. Musco.
Structure-Based Design of a B Cell Antigen from B. psuedomallei.
ACS Chem. Biol. 2015, 10(3): 803-812

[85] C. Peri, O. C. Solé, D. Corrada, A. Gori, X. Daura, G. Colombo.
Prediction of antigenic B and T cell epitopes via Energy Decomposition analysis. Description of the web-based prediction tool BEPPE. In: Peptide Antibodies: Methods and Protocols, G. Houen (Ed.)
Methods Mol. Biol. 2015, 1348: 13-22

[84] O. Conchillo-Solé, D. Yero, X. Coves, P. Huedo, S. Martínez-Servat, X. Daura, I. Gibert.
Draft genome sequence of Stenotrophomonas maltophilia strain UV74 reveals extensive variability within its genomic group.
Genome Announc. 2015, 3(3): e00611-15

2014

[83] P. Huedo, D. Yero, S. Martínez-Servat, I. Estibariz, R. Planell, P. Martínez, A. Ruyra, N. Roher, I. Roca, J. Vila, X. Daura, I. Gibert.
Two different rpf clusters distributed among a population of Stenotrophomonas maltophilia clinical strains display differential DSF production and virulence regulation.
J. Bacteriol. 2014, 196(13): 2431-2442

[82] M. V. Céspedes, U. Unzueta, W. Tatkiewicz, A. Sánchez-Chardi, O. Conchillo-Solé, P. Álamo, Z. Xu, I. Casanova, J. L. Corchero, M. Pesarrodona, J. Cedano, X. Daura, I. Ratera, J. Veciana, N. Ferrer-Miralles, E. Vazquez, A. Villaverde, R. Mangues.
In vivo Architectonic Stability of Fully de novo-Designed Protein-Only Nanoparticles.
ACS Nano 2014, 8(5): 4166-4176

[81] A. Panjkovich, X. Daura.
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.
Bioinformatics 2014, 30(9): 1314-1315

[80] P. Lassaux1, O. Conchillo-Solé, B. A. Manjasetty, D. Yero, L. Perletti, H. Belrhali, X. Daura, L. J. Gourlay, M. Bolognesi.
Redefining the PF06864 Pfam family based on Burkholderia pseudomallei PilO2Bp Sulfur-SAD crystal structure.
PLoS ONE 2014, 9(4): e94981

[79] U. Unzueta, P. Saccardo, J. Domingo-Espín, J. Cedano, O. Conchillo, E. García-Fruitós, M. V. Céspedes, J. L. Corchero, X. Daura, R. Mangues, N. Ferrer-Miralles, A. Villaverde, E. Vázquez.
Sheltering DNA in self-organizing, protein-only nano-shells as artificial viruses for gene delivery.
Nanomed. Nanotechnol. 2014, 10(3): 535-541

[78] A. Panjkovich, I. Gibert, X. Daura.
antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation.
BMC Genomics 2014, 15: 36

[77] P. Huedo, O. Conchillo-Solé, D. Yero, S. Martínez-Servat, X. Daura, I. Gibert.
Draft Genome Sequence of Stenotrophomonas maltophilia Strain M30, Isolated from a Chronic Pressure Ulcer in an Elderly Patient.
Genome Announc. 2014, 2(3): e00576-14

2013

[76] D. Urosev, M. Ferrer-Navarro, I. Pastorello, E. Cartocci, L. Costenaro, D. Zhulenkovs, J.-D. Maréchal, A. Leonchiks, D. Reverter, L. Serino, M. Soriani, X. Daura.
Crystal structure of c5321: a protective antigen present in uropathogenic Escherichia coli strains displaying an SLR fold.
BMC Struct. Biol. 2013, 13: 19

[75] L. J. Gourlay, C. Peri, M. Ferrer-Navarro, O. Conchillo-Solé, A. Gori, D. Rinchai, R. J. Thomas, O. L. Champion, S. L. Michell, C. Kewcharoenwong, A. Nithichanon, P. Lassaux, L. Perletti, R. Longhi, G. Lertmemongkolchai, R. W. Titball, X. Daura, G. Colombo, M. Bolognesi.
Exploiting the Burkholderia pseudomallei acute phase antigen BPSL2765 for structure-based epitope discovery/design in structural vaccinology.
Chemistry & Biology 2013, 20(9): 1147-1156

Featured in: Malito & Rappuoli. Finding Epitopes with Computers. Chemistry & Biology 2013, 20(10): 1205-1206

[74] I. Pastorello, S. Rossi Paccani, R. Rosini, R. Mattera, M. Ferrer-Navarro, D. Urosev, B. Nesta, P. Lo Surdo, M. Del Vecchio, V. Rippa, I. Bertoldi, D. Gomes Moriel, A. J. Laarman, J. A. G. van Strijp, X. Daura, M. Pizza, L. Serino, M. Soriani.
EsiB, a novel pathogenic Escherichia coli secretory immunoglobulin A-binding protein impairing neutrophil activation.
mBio 2013, 4(4): e00206-13

[73] M. Ferrer-Navarro, R. Planell, D. Yero, E. Mongiardini, G. Torrent, P. Huedo, P. Martínez, N. Roher, S. Mackenzie, I. Gibert, X. Daura.
Abundance of the Quorum-Sensing Factor Ax21 in Four Strains of Stenotrophomonas maltophilia Correlates with Mortality Rate in a New Zebrafish Model of Infection.
PLoS ONE 2013, 8(6): e67207

[72] A. Nuccitelli, C. D. Rinaudo, B. Brogioni, R. Cozzi, M. Ferrer-Navarro, D. Yero, J. L. Telford, G. Grandi, X. Daura, M. Zacharias, D. Maione.
Understanding the molecular determinants driving the immunological specificity of the protective pilus 2a backbone protein of Group B Streptococcus.
PLoS Comput. Biol. 2013, 9(6): e1003115

[71] P. Lassaux, C. Peri, M. Ferrer-Navarro, L. Gourlay, A. Gori, O. Conchillo-Solé, D. Rinchai, G. Lertmemongkolchai, R. Longhi, X. Daura, G. Colombo, M. Bolognesi.
A structure-based strategy for epitope discovery in Burkholderia pseudomallei OppA antigen.
Structure 2013, 21: 1-9

2012

[70] J. Domingo-Espín, V. Petegnief, N. de Vera, O. Conchillo-Solé, P. Saccardo, U. Unzueta, E. Vazquez, J. Cedano, L. Negro, X. Daura, H. Peluffo, A. M. Planas, A. Villaverde, N. Ferrer-Miralles.
RGD-based cell ligands for cell-targeted drug delivery act as potent trophic factors.
Nanomed. Nanotechnol. 2012, 8(8): 1263-1266

[69] A. Panjkovich, X. Daura.
Exploiting protein flexibility to predict the location of allosteric sites.
BMC Bioinformatics 2012, 13: 273

[68] M. Adrover, G. Martorell, S. Martin, D. Urosev, P. V. Konarev, D. Svergun, X. Daura, P. A. Temussi, A. Pastore.
The role of hydration in protein stability: comparison of the cold and heat unfolded states of Yfh1.
J. Mol. Biol. 2012, 417(5): 413-424

[67] J. Seras-Franzoso, R. Affentranger, M. Ferrer-Navarro, X. Daura, A. Villaverde, E. García-Fruitós.
Disulfide bond formation and activation of Escherichia coli β-galactosidase under oxidizing conditions.
Appl. Environ. Microbiol. 2012, 78(7): 2376-2385

2011

[66] J. Dolenc, S. Riniker, R. Gaspari, X. Daura, W. F. van Gunsteren.
Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities.
J. Comput.-Aided Mol. Des. 2011, 25(8):709-716

[65] J. Domingo-Espín, E. Vázquez, J. Ganz, O. Conchillo, E. García-Fruitós, J. Cedano, U. Unzueta, V. Petegnief, N. Gonzalez-Montalbán, A. M. Planas, X. Daura, H. Peluffo, N. Ferrer-Miralles, A. Villaverde.
Nanoparticulate architecture of protein-based artificial viruses is supported by protein-DNA interactions.
Nanomedicine 2011, 6(6): 1047-1061

[64] C. Koehler, L. Carlier, D. Veggi, E. Balducci, F. Di Marcello, M. Ferrer-Navarro, M. Pizza, X. Daura, M. Soriani, R. Boelens, A. M. J. J. Bonvin.
Structural and Biochemical Characterization of NarE, an Iron-containing ADP-ribosyltransferase from Neisseria meningitidis.
J. Biol. Chem. 2011, 286: 14842-14851

2010

[63] X. Daura, R. Affentranger, A. E. Mark.
On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences: moving particles in a condensed phase.
ChemPhysChem 2010, 11: 3734-3743

[62] M. Soriani, P. Petit, R. Grifantini, R. Petracca, G. Gancitano, E. Frigimelica, F. Nardelli, C. Garcia, S. Spinelli, G. Scarabelli, S. Fiorucci, R. Affentranger, M. Ferrer-Navarro, M. Zacharias, G. Colombo, L. Vuillard, X. Daura, G. Grandi.
Exploiting Antigenic Diversity for Vaccine Design: the Chlamydia ArtJ Paradigm.
J. Biol. Chem. 2010, 285: 30126-30138

[61] H. S. Hansen, X. Daura, P. H. Hünenberger.
Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.
J. Chem. Theor. Comput. 2010, 6: 2598-2621

[60] R. Affentranger, X. Daura.
Polypeptide folding on a conformational-space network: dependence of network topology on the structural discretization procedure.
J. Comput. Chem. 2010, 31: 1889-1903

[59] A. Panjkovich, X. Daura.
Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery.
BMC Struct. Biol. 2010, 10: 9

[58] B. Keller, X. Daura, W. F. van Gunsteren.
Comparing geometric and kinetic cluster algorithms for molecular simulation data.
J. Chem. Phys. 2010, 132: 074110

[57] E. Vázquez, M. Roldán, C. Díez-Gil, U. Unzueta, J. Domingo-Espín, J. Cedano, O. Conchillo, I. Ratera, J. Veciana, X. Daura, N. Ferrer-Miralles, A. Villaverde.
Protein nanodisk assembling and intracellular trafficking powered by an arginine-rich (R9) peptide.
Nanomedicine 2010, 5(2): 259-268

[56] S. Riniker, X. Daura, W. F. van Gunsteren.
α-Cyclodextrin Host-Guest Binding: A Computational Study of the Different Driving Forces.
Helv. Chim. Acta 2010, 93: 2318-2325

2009

[55] L. J. Gourlay, G. Colombo, M. Soriani, G. Grandi, X. Daura, M. Bolognesi.
Why is a protective antigen protective?
Human Vaccines 2009, 5(12), 872-875

[54] M. M. Reif, V. Kräutler, M. A. Kastenholz, X. Daura, P. H. Hünenberger.
Molecular Dynamics Simulations of a Reversibly Folding ß-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions.
J. Phys. Chem. B 2009, 113: 3112-3128

[53] T. A. Wassenaar, X. Daura, E. Padrós, A. E. Mark.
Calcium binding to the purple membrane: A molecular dynamics study.
Proteins: Struc. Funct. Bioinf. 2009, 74: 669-681

2008

[52] L. Muixí, M. Carrascal, I. Álvarez, X. Daura, M. Martí, M. P. Armengol, C. Pinilla, J. Abián, R. Pujol-Borrell, D. Jaraquemada.
Thyroglobulin peptides associate in vivo to HLA-DR in autoimmune thyroid glands.
J. Immunol. 2008, 181: 795-807

[51] I. Álvarez, J. Collado, X. Daura, N. Colomé, M. Rodríguez-García, T. Gallart, F. Canals, D. Jaraquemada.
The rheumatoid arthritis associated allele HLA-DR10 (DRB1*1001) shares part of its repertoire with HLA-DR1 (DRB1*0101) and HLA-DR4 (DRB*0401).
Arthritis & Rheumatism 2008, 58: 1630-1639

[50] R. Boned, W. F. van Gunsteren, X. Daura.
Estimating the temperature dependence of peptide-folding entropies and free enthalpies from total energies in molecular dynamics simulations.
Chem. Eur. J. 2008, 14: 5039-5046

2007

[49] J. H. Missimer, M. O. Steinmetz, R. Baron, F. K. Winkler, R. A. Kammerer, X. Daura, W. F. van Gunsteren.
Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.
Protein Sci. 2007, 16: 1349-1359

[48] O. Conchillo-Solé, N. Sánchez de Groot, F. X. Avilés, J. Vendrell, X. Daura, S. Ventura.
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides.
BMC Bioinformatics 2007, 8: 65

2006

[47] X. Daura.
Molecular dynamics simulation of peptide folding.
Theor. Chem. Acc. 2006; 116: 297-306

[46] W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D. P. Geerke, A. Glättli, P. H. Hünenberger, M. A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt, H. B. Yu.
Biomolecular modelling: goals, problems, perspectives.
Angew. Chem. Int. Ed. 2006; 45: 4064-4092

2005

[45] A. Glättli, X. Daura, P. Bindschädler, B. Jaun, Y. R. Mahajan, R. I. Mathad, M. Rueping, D. Seebach, W. F. van Gunsteren.
On the influence of charged side-chains on the folding-unfolding equilibrium of ß-peptides - A molecular dynamics simulation study.
Chem. Eur. J. 2005; 11: 7276-7293

[44] J. H. Missimer, M. O. Steinmetz, W. Jahnke, F. K. Winkler, W. F. van Gunsteren, X. Daura.
Molecular dynamics simulations of C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution.
Chem. Biodiv. 2005; 2: 1086-1104

[43] E. Puig, M. Garcia-Viloca, A. González-Lafont, I. López, X. Daura, J. M. Lluch.
A molecular dynamics simulation of the binding modes of D-glutamate and D-glutamine to glutamate racemase.
J. Chem. Theory and Comput. 2005; 1: 737-749

[42] A. Vera, A. Arís, X. Daura, M. A. Martínez, A. Villaverde.
Engineering the E. coli ß-galactosidase for the screening of antiviral protease-inhibitors.
Biochem. Biophys. Res. Commun. 2005; 329: 453-456

[41] P. Soto, J. Cladera, A. E. Mark, X. Daura.
Stability of SIV gp32 fusion peptide single layer protofibrils as monitored by molecular dynamics simulations.
Angew. Chem. Int. Ed. 2005; 44: 1065-1067

2004

[40] T. Soares, X. Daura, C. Oostenbrink, L. J. Smith, W. F. van Gunsteren.
Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of Hen Egg Lysozyme.
J. Biomol. NMR 2004; 30: 407-422

[39] C. M. Santiveri, M. A. Jiménez, M. Rico, W. F. van Gunsteren, X. Daura.
ß-Hairpin folding and stability: Molecular dynamics simulations of designed peptides in aqueous solution.
J. Peptide Sci. 2004; 10: 546-565

[38] A. Glättli, C. Oostenbrink, X. Daura, D. P. Geerke, H. Yu, W. F. van Gunsteren.
On the transferability of the SPC/L water model to biomolecular simulation.
Braz. J. Phys. 2004; 34: 116-125

[37] S. Calero, S. Lago, W. F. van Gunsteren, X. Daura.
Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular dynamics simulation.
Chem. Biodiv. 2004; 1: 505-519

[36] H. Yu, X. Daura, W. F. van Gunsteren.
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding and protein binding.
Proteins: Struct. Funct. Bioinf. 2004; 54: 116-127

2003

[35] X. Daura, D. Bakowies, D. Seebach, J. Fleischhauer, W. F. van Gunsteren, P. Krüger.
Circular dichroism spectra of ß-peptides: Sensitivity to molecular structure and effects of motional averaging.
Eur. Biophys. J. 2003; 32: 661-670

[34] A. Glättli, X. Daura, W. F. van Gunsteren.
A novel approach for designing simple point charge models for liquid water with three interaction sites.
J. Comput. Chem. 2003; 24: 1087-1096

[33] A. Bayés, A. Sonnenschein, X. Daura, J. Vendrell, F. X. Avilés.
Procarboxypeptidase A from the insect pest Helicoverpa armigera and its derived enzyme. Two forms with new functional properties.
Eur. J. Biochem. 2003; 270: 3026-3035

2002

[32] A. Glättli, X. Daura, D. Seebach, W. F. van Gunsteren.
Can one derive the conformational preference of a ß-peptide from its CD spectrum?
J. Am. Chem. Soc. 2002; 124: 12972-12978

[31] L. J. Smith, X. Daura, W. F. van Gunsteren.
Assessing equilibration and convergence in biomolecular simulations.
Proteins: Struct. Funct. Genet. 2002; 48: 487-496

[30] A. Glättli, X. Daura, W. F. van Gunsteren.
Derivation of an improved SPC model for liquid water: SPC/A and SPC/L.
J. Chem. Phys. 2002; 116: 9811-9828

[29] X. Daura, A. Glättli, P. Gee, C. Peter, W. F. van Gunsteren.
Unfolded state of peptides. In: Unfolded Proteins, G. D. Rose (Ed.)
Adv. Prot. Chem. 2002; 62: 341-360

[28] W. F. van Gunsteren, X. Daura, A. E. Mark.
Computation of free energy.
Helv. Chim. Acta 2002; 85: 3113-3129

[27] R. Baron, D. Bakowies, W. F. van Gunsteren, X. Daura.
ß-Peptides with different secondary structure preferences: How different are their conformational spaces?
Helv. Chim. Acta 2002; 85: 3872-3882

2001

[26] C. Peter, X. Daura, W. F. van Gunsteren.
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.
J. Biomol. NMR 2001; 20: 297-310

[25] L. D. Schuler, X. Daura, W. F. van Gunsteren.
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase.
J. Comput. Chem. 2001; 22: 1205-1218

[24] B. L. de Groot, X. Daura, A. E. Mark, H. Grubmüller.
Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds.
J. Mol. Biol. 2001; 309: 299-313

[23] H. Schäfer, X. Daura, A. E. Mark, W. F. van Gunsteren.
Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behaviour.
Proteins: Struct. Funct. Genet. 2001; 43: 45-56

[22] X. Daura, K. Gademann, H. Schäfer, B. Jaun, D. Seebach, W. F. van Gunsteren.
The ß-peptide hairpin in solution: Conformational study of a ß-hexapeptide in methanol by NMR spectroscopy and MD simulation.
J. Am. Chem. Soc. 2001; 123: 2393-2404

[21] F. A. Hamprecht, C. Peter, X. Daura, W. Thiel, W. F. van Gunsteren.
A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering and visualization.
J. Chem. Phys. 2001; 114: 2079-2089

[20] R. Bürgi, X. Daura, A. Mark, M. Bellanda, S. Mammi, E. Peggion, W. van Gunsteren.
Folding study of an aib-rich peptide in DMSO by molecular dynamics simulations.
J. Peptide Res. 2001; 57: 107-118

[19] W. F. van Gunsteren, R. Bürgi, C. Peter, X. Daura.
The key to solving the protein folding problem lies in an accurate description of the denatured state.
Angew. Chem. Int. Ed. 2001; 40: 351-355
Featured in: Nature Science Update (Protein predictors need start to finish, 30 January 2001)

[18] W.F. van Gunsteren, D. Bakowies, R. Bürgi, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, A. Glättli, T. Hansson, C. Oostenbrink, C. Peter, J. Pitera, L. Schuler, T. Soares, H. Yu.
Molecular dynamics simulation of biomolecular systems.
Chimia 2001; 55: 856-860

[17] W. Czechtizky, X. Daura, A. Vasella, W. F. van Gunsteren.
Oligonucleotide analogues with a nucleobase-including backbone. Part 7. Molecular dynamics simulation of a DNA duplex containing an 8-hydroxymethyl-2'-deoxyadenosine-derived nucleotide.
Helv. Chim. Acta 2001; 84: 2132-2145

2000

[16] B. Oliva, X. Daura, E. Querol, F. X. Avilés, O. Tapia.
A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model.
Theor. Chem. Acc. 2000; 105: 101-109

[15] C. Peter, X. Daura, W. F. van Gunsteren.
Peptides of aminoxy acids: A molecular dynamics simulation study of conformational equilibria under various conditions.
J. Am. Chem. Soc. 2000; 122: 7461-7466

[14] X. Daura, E. Haaksma, W. F. van Gunsteren.
Factor Xa: Simulation studies with an eye to inhibitor design.
J. Comput.-Aided Mol. Design 2000; 14: 507-529

[13] D. Seebach, J.V. Schreiber, S. Abele, X. Daura, W. F. van Gunsteren.
Structure and conformation of ß-oligopeptide derivatives with simple proteinogenic side-chains. Circular dichroism and molecular dynamics investigations.
Helv. Chim. Acta 2000; 83: 34-57

1999

[12] X. Daura, A. E. Mark, W. F. van Gunsteren.
Peptide folding simulations: No solvent required?
Comput. Phys. Commun. 1999; 123: 97-102

[11] X. Daura, I. Antes, W. F. van Gunsteren, W. Thiel, A. E. Mark.
The effect of motional averaging on the calculation of NMR-derived structural properties.
Proteins: Struct. Funct. Genet. 1999; 36: 542-555

[10] X. Daura, W. F. van Gunsteren, A. E. Mark.
Folding-unfolding thermodynamics of a ß-heptapeptide from equilibrium simulations.
Proteins: Struct. Funct. Genet. 1999; 34: 269-280

[9] X. Daura, R. Suter, W. F. van Gunsteren.
Validation of molecular simulation by comparison with experiment: Rotational reorientation of tryptophan in water.
J. Chem. Phys. 1999; 110: 3049-3055

[8] X. Daura, K. Gademann, B. Jaun, D. Seebach, W. F. van Gunsteren, A. E. Mark.
Peptide folding: When simulation meets experiment.
Angew. Chem. Int. Ed. 1999; 38: 236-240

1998

[7] X. Daura, B. Jaun, D. Seebach, W. F. van Gunsteren, A. E. Mark.
Reversible peptide folding in solution by molecular dynamics simulation.
J. Mol. Biol. 1998; 280: 925-932

[6] X. Daura, A. E. Mark, W. F. van Gunsteren.
Parametrization of aliphatic CHn united atoms of GROMOS96 force field.
J. Comput. Chem. 1998; 19: 535-547

1997

[5] X. Daura, W. F. van Gunsteren, D. Rigo, B. Jaun, D. Seebach.
Studying the stability of a helical ß-heptapeptide by molecular dynamics simulations.
Chem. Eur. J. 1997; 3: 1410-1417

1996

[4] X. Daura, P. H. Hünenberger, A. E. Mark, E. Querol, F. X. Avilés, W. F. van Gunsteren.
Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions.
J. Am. Chem. Soc. 1996; 118: 6285-6294

[3] X. Daura, B. Oliva, E. Querol, F. X. Avilés, O. Tapia.
On the sensitivity of MD trajectories to changes in water-protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field.
Proteins: Struct. Funct. Genet. 1996; 25: 89-103

1995

[2] B. Oliva, X. Daura, E. Querol, F. X. Avilés, O. Tapia.
Structure and atomic fluctuation patterns of potato carboxypeptidase A inhibitor protein. A molecular dynamics study in water.
Eur. Biophys. J. 1995; 24: 1-11

[1] B. Oliva, C. Marino, X. Daura, M. A. Molina, F. Canals, F. X. Avilés, E. Querol.
On the entropic and hydrophobic properties involved in the inhibitory mechanism of carboxypeptidase A by its natural inhibitor from potato.
J. Mol. Model. 1995; 1: 54-67

 

 

 

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