Mark Moll

Summary

Affiliation: Rice University
Country: USA

Publications

  1. pmc The LabelHash algorithm for substructure matching
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    BMC Bioinformatics 11:555. 2010
  2. doi request reprint The LabelHash server and tools for substructure-based functional annotation
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Bioinformatics 27:2161-2. 2011
  3. pmc SIMS: a hybrid method for rapid conformational analysis
    Bryant Gipson
    Department of Computer Science, Rice University, Houston, Texas, United States of America
    PLoS ONE 8:e68826. 2013
  4. pmc Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
    Drew H Bryant
    Department of Computer Science, Rice University, Houston, TX, USA
    BMC Bioinformatics 11:242. 2010
  5. pmc Tracing conformational changes in proteins
    Nurit Haspel
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    BMC Struct Biol 10:S1. 2010
  6. ncbi request reprint Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Comput Syst Bioinformatics Conf 7:157-68. 2008
  7. pmc Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome
    Drew H Bryant
    Department of Computer Science, Rice University, Houston, Texas, United States of America
    PLoS Comput Biol 9:e1003087. 2013
  8. pmc Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    Payel Das
    Department of Chemistry, Rice University, Houston, TX 77005, USA
    Proc Natl Acad Sci U S A 103:9885-90. 2006

Collaborators

Detail Information

Publications8

  1. pmc The LabelHash algorithm for substructure matching
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    BMC Bioinformatics 11:555. 2010
    ..However, experimental protein function determination is expensive and very time-consuming. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity...
  2. doi request reprint The LabelHash server and tools for substructure-based functional annotation
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Bioinformatics 27:2161-2. 2011
    ..The results can be downloaded for further analysis in any molecular viewer. For Chimera, there is a plugin to facilitate this process...
  3. pmc SIMS: a hybrid method for rapid conformational analysis
    Bryant Gipson
    Department of Computer Science, Rice University, Houston, Texas, United States of America
    PLoS ONE 8:e68826. 2013
    ..For all cases we provide energetic validations using well-established energy fields, demonstrating this framework as a fast and accurate tool for the analysis of a wide range of protein flexibility problems. ..
  4. pmc Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
    Drew H Bryant
    Department of Computer Science, Rice University, Houston, TX, USA
    BMC Bioinformatics 11:242. 2010
    ..In functionally homologous protein families, shared chemistry and geometry at catalytic sites provide a common, local point of comparison among proteins that may differ significantly at the sequence, fold, or domain topology levels...
  5. pmc Tracing conformational changes in proteins
    Nurit Haspel
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    BMC Struct Biol 10:S1. 2010
    ..Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions...
  6. ncbi request reprint Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction
    Mark Moll
    Department of Computer Science, Rice University, Houston, TX 77005, USA
    Comput Syst Bioinformatics Conf 7:157-68. 2008
    ..We use cluster analysis to analyze why certain classes of homologs are more difficult to classify than others. The LabelHash algorithm is implemented on a web server at http://kavrakilab.org/labelhash/...
  7. pmc Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome
    Drew H Bryant
    Department of Computer Science, Rice University, Houston, Texas, United States of America
    PLoS Comput Biol 9:e1003087. 2013
    ..Finally, these function-specific structural features may serve as potential starting points for the development of highly specific kinase inhibitors...
  8. pmc Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    Payel Das
    Department of Chemistry, Rice University, Houston, TX 77005, USA
    Proc Natl Acad Sci U S A 103:9885-90. 2006
    ..These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding...