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Ugo Bastolla - Publications

Affiliations: 
CSIC, Madrid 
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Hernández IM, Dehouck Y, Bastolla U, López-Blanco JR, Chacón P. Predicting protein stability changes upon mutation using a simple orientational potential. Bioinformatics (Oxford, England). 39. PMID 36629451 DOI: 10.1093/bioinformatics/btad011  0.548
2022 Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M. Consequences of Genetic Recombination on Protein Folding Stability. Journal of Molecular Evolution. 91: 33-45. PMID 36463317 DOI: 10.1007/s00239-022-10080-2  0.72
2019 Pascual-García A, Arenas M, Bastolla U. The Molecular Clock in the Evolution of Protein Structures. Systematic Biology. PMID 31111152 DOI: 10.1093/sysbio/syz022  0.702
2019 Bastolla U, Arenas M. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. Methods in Molecular Biology (Clifton, N.J.). 1851: 215-231. PMID 30298399 DOI: 10.1007/978-1-4939-8736-8_11  0.766
2018 Jiménez-Santos MJ, Arenas M, Bastolla U. Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. Peerj. 6: e5549. PMID 30310736 DOI: 10.7717/peerj.5549  0.709
2017 Jimenez MJ, Arenas M, Bastolla U. Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data. Molecular Biology and Evolution. PMID 29294047 DOI: 10.1093/molbev/msx327  0.744
2017 Arenas M, Weber CC, Liberles DA, Bastolla U. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology. PMID 28057858 DOI: 10.1093/Sysbio/Syw121  0.775
2015 Arenas M, Sánchez-Cobos A, Bastolla U. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. Molecular Biology and Evolution. 32: 2195-207. PMID 25837579 DOI: 10.1093/molbev/msv085  0.712
2014 Treviño MA, García-Mayoral MF, Jiménez MÁ, Bastolla U, Bruix M. Emergence of structure through protein-protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins. Biochimica Et Biophysica Acta. 1844: 1808-19. PMID 25091198 DOI: 10.1016/j.bbapap.2014.07.019  0.439
2013 Arenas M, Dos Santos HG, Posada D, Bastolla U. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics (Oxford, England). 29: 3020-8. PMID 24037213 DOI: 10.1093/Bioinformatics/Btt530  0.722
2013 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, ... ... Bastolla U, et al. Structure and non-structure of centrosomal proteins. Plos One. 8: e62633. PMID 23671615 DOI: 10.1371/Journal.Pone.0062633  0.461
2013 Dos Santos HG, Klett J, Méndez R, Bastolla U. Characterizing conformation changes in proteins through the torsional elastic response. Biochimica Et Biophysica Acta. 1834: 836-46. PMID 23429178 DOI: 10.1016/j.bbapap.2013.02.010  0.331
2012 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, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  0.644
2010 Mendez R, Fritsche M, Porto M, Bastolla U. Mutation bias favors protein folding stability in the evolution of small populations. Plos Computational Biology. 6: e1000767. PMID 20463869 DOI: 10.1371/journal.pcbi.1000767  0.464
2010 Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U. Quantifying the evolutionary divergence of protein structures: the role of function change and function conservation. Proteins. 78: 181-96. PMID 19830831 DOI: 10.1002/prot.22616  0.499
2008 Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR. An efficient conformational sampling method for homology modeling Proteins: Structure, Function and Genetics. 71: 175-188. PMID 17985353 DOI: 10.1002/Prot.21672  0.318
2006 Bastolla U, Porto M, Roman HE, Vendruscolo M. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. Bmc Evolutionary Biology. 6: 43-43. PMID 16737532 DOI: 10.1186/1471-2148-6-43  0.599
2005 Bastolla U, Porto M, Roman HE, Vendruscolo M. Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles. Gene. 347: 219-230. PMID 15777696 DOI: 10.1016/J.Gene.2004.12.015  0.639
2005 Porto M, Roman HE, Vendruscolo M, Bastolla U. Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences Molecular Biology and Evolution. 22: 630-638. PMID 15537801 DOI: 10.1093/Molbev/Msi048  0.616
2004 Bastolla U, Porto M, Roman HE, Vendruscolo M. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins. 58: 22-30. PMID 15523667 DOI: 10.1002/Prot.20240  0.462
2004 Bastolla U, Moya A, Viguera E, Ham RCHJv. Genomic determinants of protein folding thermodynamics in prokaryotic organisms. Journal of Molecular Biology. 343: 1451-1466. PMID 15491623 DOI: 10.1016/J.Jmb.2004.08.086  0.505
2004 Porto M, Bastolla U, Roman HE, Vendruscolo M. Reconstruction of protein structures from a vectorial representation. Physical Review Letters. 92: 218101. PMID 15245321 DOI: 10.1103/Physrevlett.92.218101  0.358
2003 Bastolla U, Porto M, Roman HE, Vendruscolo M. Statistical properties of neutral evolution. Journal of Molecular Evolution. 57. PMID 15008407 DOI: 10.1007/S00239-003-0013-4  0.537
2003 Bastolla U, Porto M, Roman HE, Vendruscolo M. Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. Journal of Molecular Evolution. 56: 243-254. PMID 12612828 DOI: 10.1007/S00239-002-2350-0  0.592
2003 van Ham RC, Kamerbeek J, Palacios C, Rausell C, Abascal F, Bastolla U, Fernández JM, Jiménez L, Postigo M, Silva FJ, Tamames J, Viguera E, Latorre A, Valencia A, Morán F, et al. Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences of the United States of America. 100: 581-6. PMID 12522265 DOI: 10.1073/Pnas.0235981100  0.32
2003 Wallin S, Farwer J, Bastolla U. Testing similarity measures with continuous and discrete protein models. Proteins. 50: 144-57. PMID 12471607 DOI: 10.1002/prot.10271  0.344
2002 Bastolla U, Porto M, Roman HE, Vendruscolo M. Lack of self-averaging in neutral evolution of proteins. Physical Review Letters. 89: 208101. PMID 12443510 DOI: 10.1103/Physrevlett.89.208101  0.548
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