Pengyu Ren

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. ncbi Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases
    Michael J Schnieders
    Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Curr Pharm Des 18:1173-85. 2012
  2. ncbi Conformational preference of ChaK1 binding peptides: a molecular dynamics study
    Jiajing Zhang
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
    PMC Biophys 3:2. 2010
  3. ncbi A model of a MAPK•substrate complex in an active conformation: a computational and experimental approach
    Sunbae Lee
    Division of Medicinal Chemistry, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 6:e18594. 2011
  4. ncbi Trypsin-ligand binding free energy calculation with AMOEBA
    Yue Shi
    Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:2328-31. 2009
  5. ncbi Virtual screening using molecular simulations
    Tianyi Yang
    Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
    Proteins 79:1940-51. 2011
  6. ncbi Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1
    Chunli Yan
    Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
    J Phys Chem B 115:1491-502. 2011
  7. ncbi Multipole electrostatics in hydration free energy calculations
    Yue Shi
    Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
    J Comput Chem 32:967-77. 2011
  8. ncbi Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
    Johnny Wu
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 1062, USA
    J Chem Phys 135:155104. 2011
  9. ncbi Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1
    Kari Callaway
    Division of Medicinal Chemistry, University of Texas, Austin, Texas 78712, USA
    Biochemistry 49:3619-30. 2010
  10. ncbi Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation
    Chunli Yan
    Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA
    J Mol Graph Model 29:2-12. 2010

Research Grants

  1. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2007
  2. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2009
  3. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2010

Collaborators

  • Yue Shi
  • Chunli Yan
  • Kevin N Dalby
  • Michael J Schnieders
  • Sunbae Lee
  • Jiajing Zhang
  • Tamer S Kaoud
  • David P Gardner
  • Johnny Wu
  • Tianyi Yang
  • Guohui Li
  • Kari Callaway
  • Dian Jiao
  • Ray Luo
  • Robin R Gutell
  • Tamer Kaoud
  • Hujun Shen
  • Johnny C Wu
  • Ranajeet Ghose
  • Xia Zhen
  • Mangalika Warthaka
  • Michael B Gonzales
  • Andrea Piserchio
  • Yuanfeng Wang
  • Stuart Ozer
  • Kevin Dalby
  • Mark A Rainey
  • James W Tunnell
  • Varun Pattani
  • William F Waas
  • Christopher A King
  • Robert E Duke

Detail Information

Publications13

  1. ncbi Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases
    Michael J Schnieders
    Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Curr Pharm Des 18:1173-85. 2012
    ..The impact of an advanced polarizable force field such as AMOEBA used in conjunction with sophisticated kinetic and thermodynamic simulation methods is also discussed...
  2. ncbi Conformational preference of ChaK1 binding peptides: a molecular dynamics study
    Jiajing Zhang
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
    PMC Biophys 3:2. 2010
    ..The key structural elements, sequence motifs, and amino acid residues in the ChaK1 and their possible functions involved in the substrate recognition are discussed.PACS Codes: 87.15.A-..
  3. ncbi A model of a MAPK•substrate complex in an active conformation: a computational and experimental approach
    Sunbae Lee
    Division of Medicinal Chemistry, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 6:e18594. 2011
    ..Our kinetic analysis suggests that the unstructured N-terminus provides 10-fold uniform stabilization of the ground state ERK2•Ets•MgATP complex and intermediates of the enzymatic reaction...
  4. ncbi Trypsin-ligand binding free energy calculation with AMOEBA
    Yue Shi
    Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:2328-31. 2009
    ..While the binding free energy is independent of the ligand dipole moment, it shows a strong correlation with the ligand molecular polarizability...
  5. ncbi Virtual screening using molecular simulations
    Tianyi Yang
    Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
    Proteins 79:1940-51. 2011
    ..Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery...
  6. ncbi Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1
    Chunli Yan
    Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
    J Phys Chem B 115:1491-502. 2011
    ..We have performed experiments using purified JNK1 to confirm that, indeed, D-pepJIP1 does not inhibit the ability of JNK1 to phosphorylate c-Jun in vitro...
  7. ncbi Multipole electrostatics in hydration free energy calculations
    Yue Shi
    Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
    J Comput Chem 32:967-77. 2011
    ..In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the HFE calculation...
  8. ncbi Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent
    Johnny Wu
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 1062, USA
    J Chem Phys 135:155104. 2011
    ..The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling...
  9. ncbi Phosphorylation of the transcription factor Ets-1 by ERK2: rapid dissociation of ADP and phospho-Ets-1
    Kari Callaway
    Division of Medicinal Chemistry, University of Texas, Austin, Texas 78712, USA
    Biochemistry 49:3619-30. 2010
    ..A molecular mechanics model of the complex formed between ERK2 and residues 28-138 of Ets-1 provides insight into the role of substrate docking interactions...
  10. ncbi Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation
    Chunli Yan
    Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA
    J Mol Graph Model 29:2-12. 2010
    ....
  11. ncbi Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure
    David P Gardner
    Center for Computational Biology and Bioinformatics, Section of Integrative Biology in the School of Biological Sciences, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Biol 413:473-83. 2011
    ..Overall, these new statistical potentials for hairpin and internal loops integrated into the new version of RNAfold demonstrated significant improvements in the prediction accuracy of RNA secondary structure...
  12. ncbi Probing the Effect of Conformational Constraint on Phosphorylated Ligand Binding to an SH2 Domain Using Polarizable Force Field Simulations
    Yue Shi
    Department of Biomedical Engineering and Department of Chemistry and Biochemistry, The University of Texas at Austin, Texas 78712, United States
    J Phys Chem B 116:1716-27. 2012
    ....
  13. ncbi Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential
    Dian Jiao
    Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
    J Comput Chem 30:1701-11. 2009
    ..Overall the relative binding free energies obtained from the MM-PMPB/SA model are in good agreement with the experimental data...

Research Grants4

  1. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2007
    ....
  2. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2009
    ....
  3. Computational Drug Discovery with Polarizable Potential Eneergy Function
    Pengyu Ren; Fiscal Year: 2010
    ....