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Items: 1 to 50 of 63

1.

The Molecular Clock in the Evolution of Protein Structures.

Pascual-García A, Arenas M, Bastolla U.

Syst Biol. 2019 Apr 23. pii: syz022. doi: 10.1093/sysbio/syz022. [Epub ahead of print]

PMID:
31111152
2.

Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery.

Alfayate A, Caceres CR, Gomes Dos Santos H, Bastolla U.

Bioinformatics. 2019 Apr 30. pii: btz301. doi: 10.1093/bioinformatics/btz301. [Epub ahead of print]

PMID:
31038697
3.

Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins.

Sequeira-Mendes J, Vergara Z, Peiró R, Morata J, Aragüez I, Costas C, Mendez-Giraldez R, Casacuberta JM, Bastolla U, Gutierrez C.

Genome Res. 2019 May;29(5):784-797. doi: 10.1101/gr.240986.118. Epub 2019 Mar 7.

PMID:
30846531
4.

Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution.

Jiménez-Santos MJ, Arenas M, Bastolla U.

PeerJ. 2018 Oct 5;6:e5549. doi: 10.7717/peerj.5549. eCollection 2018.

5.

The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference.

Bastolla U, Arenas M.

Methods Mol Biol. 2019;1851:215-231. doi: 10.1007/978-1-4939-8736-8_11.

PMID:
30298399
6.

Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data.

Jimenez MJ, Arenas M, Bastolla U.

Mol Biol Evol. 2017 Dec 26. doi: 10.1093/molbev/msx327. [Epub ahead of print]

PMID:
29294047
7.

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
8.

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.

9.

Mutualism supports biodiversity when the direct competition is weak.

Pascual-García A, Bastolla U.

Nat Commun. 2017 Feb 24;8:14326. doi: 10.1038/ncomms14326.

10.

Editorial overview: Proteins: bridging theory and experiment.

Berezovsky IN, Bastolla U.

Curr Opin Struct Biol. 2017 Feb;42:viii-x. doi: 10.1016/j.sbi.2016.12.013. Epub 2017 Jan 10. No abstract available.

PMID:
28087119
11.

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

Arenas M, Weber CC, Liberles DA, Bastolla U.

Syst Biol. 2017 Nov 1;66(6):1054-1064. doi: 10.1093/sysbio/syw121.

PMID:
28057858
12.

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
13.

Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.

Arenas M, Sánchez-Cobos A, Bastolla U.

Mol Biol Evol. 2015 Aug;32(8):2195-207. doi: 10.1093/molbev/msv085. Epub 2015 Apr 2.

14.

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

Pascual-García A, Tamames J, Bastolla U.

BMC Microbiol. 2014 Dec 4;14:284. doi: 10.1186/s12866-014-0284-5.

15.

Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins.

Treviño MA, García-Mayoral MF, Jiménez MÁ, Bastolla U, Bruix M.

Biochim Biophys Acta. 2014 Oct;1844(10):1808-19. doi: 10.1016/j.bbapap.2014.07.019. Epub 2014 Aug 1.

PMID:
25091198
16.

Detecting selection on protein stability through statistical mechanical models of folding and evolution.

Bastolla U.

Biomolecules. 2014 Mar 7;4(1):291-314. doi: 10.3390/biom4010291. Review.

17.

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States.

Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C.

Plant Cell. 2014 Jun;26(6):2351-2366. Epub 2014 Jun 16.

18.

Protein evolution along phylogenetic histories under structurally constrained substitution models.

Arenas M, Dos Santos HG, Posada D, Bastolla U.

Bioinformatics. 2013 Dec 1;29(23):3020-8. doi: 10.1093/bioinformatics/btt530. Epub 2013 Sep 12.

19.

High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins.

Lombraña R, Almeida R, Revuelta I, Madeira S, Herranz G, Saiz N, Bastolla U, Gómez M.

EMBO J. 2013 Oct 2;32(19):2631-44. doi: 10.1038/emboj.2013.195. Epub 2013 Aug 30.

20.

Structure and non-structure of centrosomal proteins.

Dos Santos HG, Abia D, Janowski R, Mortuza G, Bertero MG, Boutin M, Guarín N, Méndez-Giraldez R, Nuñez A, Pedrero JG, Redondo P, Sanz M, Speroni S, Teichert F, Bruix M, Carazo JM, Gonzalez C, Reina J, Valpuesta JM, Vernos I, Zabala JC, Montoya G, Coll M, Bastolla U, Serrano L.

PLoS One. 2013 May 9;8(5):e62633. doi: 10.1371/journal.pone.0062633. Print 2013.

21.

The emerging dynamic view of proteins: protein plasticity in allostery, evolution and self-assembly.

Bastolla U, Porto M, Roman HE.

Biochim Biophys Acta. 2013 May;1834(5):817-9. doi: 10.1016/j.bbapap.2013.03.016. No abstract available.

PMID:
23587551
22.

Characterizing conformation changes in proteins through the torsional elastic response.

Dos Santos HG, Klett J, Méndez R, Bastolla U.

Biochim Biophys Acta. 2013 May;1834(5):836-46. doi: 10.1016/j.bbapap.2013.02.010. Epub 2013 Feb 19.

PMID:
23429178
23.

Detecting selection for negative design in proteins through an improved model of the misfolded state.

Minning J, Porto M, Bastolla U.

Proteins. 2013 Jul;81(7):1102-12. doi: 10.1002/prot.24244. Epub 2013 Apr 10.

PMID:
23280507
24.

Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding.

Bastolla U, Bruscolini P, Velasco JL.

Proteins. 2012 Aug;80(9):2287-304. doi: 10.1002/prot.24118. Epub 2012 Jun 18.

PMID:
22623399
25.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

26.

Protein disorder in the centrosome correlates with complexity in cell types number.

Nido GS, Méndez R, Pascual-García A, Abia D, Bastolla U.

Mol Biosyst. 2012 Jan;8(1):353-67. doi: 10.1039/c1mb05199g. Epub 2011 Nov 11.

PMID:
22076659
27.

Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins.

Mendez R, Bastolla U.

Phys Rev Lett. 2010 Jun 4;104(22):228103. Epub 2010 Jun 3.

PMID:
20867208
28.

Comparison of translation loads for standard and alternative genetic codes.

Sammet SG, Bastolla U, Porto M.

BMC Evol Biol. 2010 Jun 14;10:178. doi: 10.1186/1471-2148-10-178.

29.

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

Teichert F, Minning J, Bastolla U, Porto M.

BMC Bioinformatics. 2010 May 14;11:251. doi: 10.1186/1471-2105-11-251.

30.

Mutation bias favors protein folding stability in the evolution of small populations.

Mendez R, Fritsche M, Porto M, Bastolla U.

PLoS Comput Biol. 2010 May 6;6(5):e1000767. doi: 10.1371/journal.pcbi.1000767.

31.

In memoriam. Angel Ramírez Ortiz (1966-2008).

Abia D, Bastolla U, Chacón P, Fábrega C, Gago F, Morreale A, Tramontano A.

Proteins. 2010 Jan;78(1):iii-viii. doi: 10.1002/prot.22660. No abstract available.

PMID:
19937956
32.

Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation.

Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U.

Proteins. 2010 Jan;78(1):181-96. doi: 10.1002/prot.22616.

PMID:
19830831
33.

The architecture of mutualistic networks minimizes competition and increases biodiversity.

Bastolla U, Fortuna MA, Pascual-García A, Ferrera A, Luque B, Bascompte J.

Nature. 2009 Apr 23;458(7241):1018-20. doi: 10.1038/nature07950.

PMID:
19396144
34.

Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.

Pascual-García A, Abia D, Ortiz AR, Bastolla U.

PLoS Comput Biol. 2009 Mar;5(3):e1000331. doi: 10.1371/journal.pcbi.1000331. Epub 2009 Mar 27.

35.

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.

Bastolla U, Ortíz AR, Porto M, Teichert F.

Proteins. 2008 Dec;73(4):872-88. doi: 10.1002/prot.22113.

PMID:
18536008
36.

An efficient conformational sampling method for homology modeling.

Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR.

Proteins. 2008 Apr;71(1):175-88.

PMID:
17985353
37.

SABERTOOTH: protein structural alignment based on a vectorial structure representation.

Teichert F, Bastolla U, Porto M.

BMC Bioinformatics. 2007 Oct 31;8:425.

38.

Local interactions in protein folding determined through an inverse folding model.

Bastolla U, Porto M, Ortíz AR.

Proteins. 2008 Apr;71(1):278-99. Erratum in: Proteins. 2008 Sep;72(4):1377.

PMID:
17932940
39.
40.

Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds.

Bastolla U, Demetrius L.

Protein Eng Des Sel. 2005 Sep;18(9):405-15. Epub 2005 Aug 5.

PMID:
16085657
41.

Biodiversity in model ecosystems, II: species assembly and food web structure.

Bastolla U, Lässig M, Manrubia SC, Valleriani A.

J Theor Biol. 2005 Aug 21;235(4):531-9. Epub 2005 Mar 23.

PMID:
15935171
42.

Biodiversity in model ecosystems, I: coexistence conditions for competing species.

Bastolla U, Lässig M, Manrubia SC, Valleriani A.

J Theor Biol. 2005 Aug 21;235(4):521-30. Epub 2005 Mar 31.

PMID:
15935170
43.
44.

Protein evolution in viral quasispecies under selective pressure: a thermodynamic and phylogenetic analysis.

Briones C, Bastolla U.

Gene. 2005 Mar 14;347(2):237-46. Epub 2005 Feb 17.

PMID:
15725390
45.

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences.

Porto M, Roman HE, Vendruscolo M, Bastolla U.

Mol Biol Evol. 2005 Mar;22(3):630-8. Epub 2004 Nov 10. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1156. Mol Biol Evol. 2005 Apr;22(4):1159.

PMID:
15537801
46.

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins.

Bastolla U, Porto M, Roman HE, Vendruscolo M.

Proteins. 2005 Jan 1;58(1):22-30.

PMID:
15523667
47.

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

Bastolla U, Moya A, Viguera E, van Ham RC.

J Mol Biol. 2004 Nov 5;343(5):1451-66.

PMID:
15491623
48.

Reconstruction of protein structures from a vectorial representation.

Porto M, Bastolla U, Roman HE, Vendruscolo M.

Phys Rev Lett. 2004 May 28;92(21):218101. Epub 2004 May 28.

PMID:
15245321
49.

Statistical properties of neutral evolution.

Bastolla U, Porto M, Roman HE, Vendruscolo M.

J Mol Evol. 2003;57 Suppl 1:S103-19.

PMID:
15008407
50.

Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution.

Bastolla U, Porto M, Eduardo Roman MH, Vendruscolo MH.

J Mol Evol. 2003 Mar;56(3):243-54.

PMID:
12612828

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