Markus Porto

Summary

Affiliation: Darmstadt University of Technology
Country: Germany

Publications

  1. ncbi request reprint Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    Ugo Bastolla
    Centro de Astrobiología INTA CSIC, 28850 Torrejon de Ardoz, Spain
    Proteins 58:22-30. 2005
  2. pmc A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
    Ugo Bastolla
    Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Cantoblanco, 28049 Madrid, Spain
    BMC Evol Biol 6:43. 2006
  3. pmc Stochastic reconstruction of protein structures from effective connectivity profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany
    PMC Biophys 1:5. 2008
  4. ncbi request reprint Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
    Markus Porto
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr 8, 64289 Darmstadt, Germany
    Mol Biol Evol 22:630-8. 2005
  5. pmc High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH
    Florian Teichert
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, Darmstadt, Germany
    BMC Bioinformatics 11:251. 2010
  6. doi request reprint Detecting selection for negative design in proteins through an improved model of the misfolded state
    Jonas Minning
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Darmstadt, Germany
    Proteins 81:1102-12. 2013
  7. pmc Comparison of translation loads for standard and alternative genetic codes
    Stefanie Gabriele Sammet
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, 8, 64289 Darmstadt, Germany
    BMC Evol Biol 10:178. 2010
  8. doi request reprint Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, 64289 Darmstadt, Germany
    Proteins 78:249-58. 2010
  9. ncbi request reprint A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany
    Gene 422:47-51. 2008
  10. pmc SABERTOOTH: protein structural alignment based on a vectorial structure representation
    Florian Teichert
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, 6 8, 64289 Darmstadt, Germany
    BMC Bioinformatics 8:425. 2007

Collaborators

Detail Information

Publications16

  1. ncbi request reprint Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    Ugo Bastolla
    Centro de Astrobiología INTA CSIC, 28850 Torrejon de Ardoz, Spain
    Proteins 58:22-30. 2005
    ..We show that the interactivity scale is nearly optimal both for the comparison of sequences to sequences and sequences to structures...
  2. pmc A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
    Ugo Bastolla
    Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Cantoblanco, 28049 Madrid, Spain
    BMC Evol Biol 6:43. 2006
    ..However, models of molecular evolution that aim at reconstructing the evolutionary history of macromolecules become computationally intractable if such correlations between sites are explicitly taken into account...
  3. pmc Stochastic reconstruction of protein structures from effective connectivity profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany
    PMC Biophys 1:5. 2008
    ..PACS codes: 87.14.Ee...
  4. ncbi request reprint Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
    Markus Porto
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr 8, 64289 Darmstadt, Germany
    Mol Biol Evol 22:630-8. 2005
    ..The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, as a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case...
  5. pmc High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH
    Florian Teichert
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, Darmstadt, Germany
    BMC Bioinformatics 11:251. 2010
    ..This situation demands development of methods that extend the applicability of accurate sequence alignment to distantly related proteins...
  6. doi request reprint Detecting selection for negative design in proteins through an improved model of the misfolded state
    Jonas Minning
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Darmstadt, Germany
    Proteins 81:1102-12. 2013
    ..Applying this model, we detect and quantify selection for negative design in most natural proteins, and we analytically design protein sequences that are stable both against unfolding and against misfolding...
  7. pmc Comparison of translation loads for standard and alternative genetic codes
    Stefanie Gabriele Sammet
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, 8, 64289 Darmstadt, Germany
    BMC Evol Biol 10:178. 2010
    ..It has been shown that the standard genetic code is preferential to randomly assembled codes for its ability to reduce the effects of errors in protein translation...
  8. doi request reprint Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, 64289 Darmstadt, Germany
    Proteins 78:249-58. 2010
    ..We show here that the use of structural profiles, which can be predicted with good accuracy from the amino acid sequences of proteins, provides an efficient means to identify good candidate structures...
  9. ncbi request reprint A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles
    Katrin Wolff
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany
    Gene 422:47-51. 2008
    ..Our results indicate that an accurate physico-chemical energy function should be used in conjunction with the structural profile bias in order to achieve accurate reconstructions...
  10. pmc SABERTOOTH: protein structural alignment based on a vectorial structure representation
    Florian Teichert
    Institut fur Festkorperphysik, Technische Universitat Darmstadt, Hochschulstr, 6 8, 64289 Darmstadt, Germany
    BMC Bioinformatics 8:425. 2007
    ..These decrease the effort of comparing large sets of coordinates, but protein structural alignment still remains computationally expensive...
  11. ncbi request reprint Lack of self-averaging in neutral evolution of proteins
    Ugo Bastolla
    Centro de Astrobiología INTA CSIC, 28850 Torrejon de Ardoz, Spain
    Phys Rev Lett 89:208101. 2002
    ..Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process...
  12. ncbi request reprint Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles
    Ugo Bastolla
    Centro de Astrobiologia, INTA CSIC, c tra de Ajalvir km 4, E 28850, Torrejon de Ardoz, Madrid, Spain
    Gene 347:219-30. 2005
    ..Interestingly, the optimal model almost minimizes the rate at which deleterious mutations are eliminated by natural selection...
  13. ncbi request reprint Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution
    Ugo Bastolla
    Centro de Astrobiología INTA CSIC, c tra de Ajalvir km 4, 28850 Torrejon de Ardoz, Spain
    J Mol Evol 56:243-54. 2003
    ..These results indicate that a synergy between database analysis and structurally based computational studies can increase our understanding of protein evolution...
  14. ncbi request reprint Reconstruction of protein structures from a vectorial representation
    Markus Porto
    Max Planck Institut fur Physik komplexer Systeme, Nothnitzer Strasse 38, 01187 Dresden, Germany
    Phys Rev Lett 92:218101. 2004
    ..This representation is expected to provide a useful tool in bioinformatics algorithms for protein structure comparison and alignment, as well as a promising intermediate step towards protein structure prediction...
  15. ncbi request reprint Statistical properties of neutral evolution
    Ugo Bastolla
    Centro de Astrobiología INTA CSIC, 28850 Torrejon de Ardoz, Spain
    J Mol Evol 57:S103-19. 2003
    ..In particular, we compute the minimal sequence similarity below which no information about the evolutionary divergence of the compared sequences can be obtained...
  16. ncbi request reprint Local interactions in protein folding determined through an inverse folding model
    Ugo Bastolla
    Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Cantoblanco, 28049 Madrid, Spain
    Proteins 71:278-99. 2008
    ..This work highlights the importance to apply more challenging tests, as the recognition of homologous structures, for testing stability scores for protein folding...