Angel R Ortiz

Summary

Affiliation: Mount Sinai School of Medicine
Country: USA

Publications

  1. pmc MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison
    Angel R Ortiz
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA
    Protein Sci 11:2606-21. 2002
  2. ncbi request reprint A new progressive-iterative algorithm for multiple structure alignment
    Dmitry Lupyan
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Bioinformatics 21:3255-63. 2005
  3. pmc Gene discovery in bladder cancer progression using cDNA microarrays
    Marta Sanchez-Carbayo
    Division of Molecular Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Am J Pathol 163:505-16. 2003
  4. ncbi request reprint Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors
    Marta Murcia
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, One Gustave Levy Place, Box 1218, New York, New York 10029, USA
    J Med Chem 47:805-20. 2004
  5. ncbi request reprint Gaussian mapping of chemical fragments in ligand binding sites
    Kun Wang
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave Levy Pl, Box 1218, New York, NY 10029, USA
    J Comput Aided Mol Des 18:101-18. 2004
  6. ncbi request reprint Core deformations in protein families: a physical perspective
    Alejandra Leo-Macias
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco 28049, Madrid, Spain
    Biophys Chem 115:125-8. 2005
  7. pmc An analysis of core deformations in protein superfamilies
    Alejandra Leo-Macias
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Cantoblanco, Madrid, Spain
    Biophys J 88:1291-9. 2005
  8. ncbi request reprint An efficient conformational sampling method for homology modeling
    Rongsheng Han
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco, Madrid, Spain
    Proteins 71:175-88. 2008
  9. pmc Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold
    Francisco J Blanco
    NMR Group, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
    Protein Sci 13:1458-65. 2004
  10. ncbi request reprint CAFASP3: the third critical assessment of fully automated structure prediction methods
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:503-16. 2003

Collaborators

Detail Information

Publications12

  1. pmc MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison
    Angel R Ortiz
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA
    Protein Sci 11:2606-21. 2002
    ..Overall, our results indicate that the new program (MAMMOTH) will be a good tool for protein structure comparisons in structural genomics applications. MAMMOTH is available from our web site at http://physbio.mssm.edu/~ortizg/...
  2. ncbi request reprint A new progressive-iterative algorithm for multiple structure alignment
    Dmitry Lupyan
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA
    Bioinformatics 21:3255-63. 2005
    ....
  3. pmc Gene discovery in bladder cancer progression using cDNA microarrays
    Marta Sanchez-Carbayo
    Division of Molecular Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Am J Pathol 163:505-16. 2003
    ..The present study has identified molecular biomarkers of potential clinical significance and critical molecular targets associated with bladder cancer progression...
  4. ncbi request reprint Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors
    Marta Murcia
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, One Gustave Levy Place, Box 1218, New York, New York 10029, USA
    J Med Chem 47:805-20. 2004
    ..In our best case, a recognition rate of approximately 80% of known binders at approximately 15% false positives rate was achieved, corresponding to an enrichment factor of approximately 450% over random...
  5. ncbi request reprint Gaussian mapping of chemical fragments in ligand binding sites
    Kun Wang
    Department of Physiology and Biophysics, Mount Sinai School of Medicine, One Gustave Levy Pl, Box 1218, New York, NY 10029, USA
    J Comput Aided Mol Des 18:101-18. 2004
    ..An average 4-5-fold speed-up in docking times and a similar success rate is estimated with respect to the standard DOCK protocol...
  6. ncbi request reprint Core deformations in protein families: a physical perspective
    Alejandra Leo-Macias
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco 28049, Madrid, Spain
    Biophys Chem 115:125-8. 2005
    ..The findings have implications in structure prediction by homology modeling...
  7. pmc An analysis of core deformations in protein superfamilies
    Alejandra Leo-Macias
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC UAM, Cantoblanco, Madrid, Spain
    Biophys J 88:1291-9. 2005
    ..The findings have implications in structure prediction by homology modeling...
  8. ncbi request reprint An efficient conformational sampling method for homology modeling
    Rongsheng Han
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco, Madrid, Spain
    Proteins 71:175-88. 2008
    ..Applications and limitations of this methodology are finally discussed...
  9. pmc Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold
    Francisco J Blanco
    NMR Group, Centro Nacional de Investigaciones Oncologicas, Madrid, Spain
    Protein Sci 13:1458-65. 2004
    ..coli...
  10. ncbi request reprint CAFASP3: the third critical assessment of fully automated structure prediction methods
    Daniel Fischer
    Bioinformatics, Department of Computer Science, Ben Gurion University, Beer Sheva, Israel
    Proteins 53:503-16. 2003
    ..This result shows that significant progress has been achieved in automatic structure prediction and has important implications to the prospects of automated structure modeling in the context of structural genomics...
  11. ncbi request reprint A new implicit solvent model for protein-ligand docking
    Antonio Morreale
    Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma de Madrid, Cantoblanco, Madrid 28049, Spain
    Proteins 67:606-16. 2007
    ..Computation times of approximately 0.030 s per pose are obtained on a single processor desktop workstation...
  12. pmc Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
    Bin Qian
    Howard Hughes Medical Institute and Department of Biochemistry, University of Washington, J 567 Health Sciences, Box 357350, Seattle, WA 98105, USA
    Proc Natl Acad Sci U S A 101:15346-51. 2004
    ....