Matthew P. Jacobson

19 papers Journal 19
YearRankTypeTitle / Venue / Authors
2016 J jnl
Defining the Product Chemical Space of Monoterpenoid Synthases.
PLoS Comput. Biol.
Bo-Xue Tian, C. Dale Poulter, Matthew P. Jacobson
2016 J jnl
Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction.
J. Chem. Inf. Model.
Qin Wang, Simone Sciabola, Gabriela Barreiro, Xinjun Hou, Guoyun Bai, Michael J. Shapiro, Frank Koehn, Anabella Villalobos, Matthew P. Jacobson
2016 J jnl
Non-degradative Ubiquitination of Protein Kinases.
PLoS Comput. Biol.
K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson
2016 J jnl
Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition.
J. Chem. Inf. Model.
Siegfried S. F. Leung, Daniel J. Sindhikara, Matthew P. Jacobson
2014 J jnl
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach.
PLoS Comput. Biol.
Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
2014 J jnl
Prediction of Substrates for Glutathione Transferases by Covalent Docking.
J. Chem. Inf. Model.
Guang Qiang Dong, Sara Calhoun, Hao Fan, Chakrapani Kalyanaraman, Megan C. Branch, Susan T. Mashiyama, Nir London, Matthew P. Jacobson, Patricia C. Babbitt, Brian K. Shoichet, Richard N. Armstrong, Andrej Sali
2014 J jnl
The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery.
PLoS Comput. Biol.
Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson
2013 J jnl
Discovery of new enzymes and metabolic pathways by using structure and genome context.
Nat.
Suwen Zhao, Ritesh Kumar, Ayano Sakai, Matthew W. Vetting, B. McKay Wood, Shoshana D. Brown, Jeffery B. Bonanno, Brandan S. Hillerich, Ronald D. Seidel, Patricia C. Babbitt, Steven C. Almo, Jonathan V. Sweedler, John A. Gerlt, John E. Cronan, Matthew P. Jacobson
2012 J jnl
Testing Physical Models of Passive Membrane Permeation.
J. Chem. Inf. Model.
Siegfried S. F. Leung, Jona Mijalkovic, Kenneth W. Borrelli, Matthew P. Jacobson
2011 J jnl
A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series.
J. Chem. Inf. Model.
Chaya Rapp, Chakrapani Kalyanaraman, Aviva Schiffmiller, Esther Leah Schoenbrun, Matthew P. Jacobson
2011 J jnl
A New View of the Bacterial Cytosol Environment.
PLoS Comput. Biol.
Benjamin P. Cossins, Matthew P. Jacobson, Victor Guallar
2011 J jnl
Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation.
PLoS Comput. Biol.
Arjun Narayanan, Lawrence L. LeClaire III, Diane L. Barber, Matthew P. Jacobson
2011 J jnl
Predicting Binding to P-Glycoprotein by Flexible Receptor Docking.
PLoS Comput. Biol.
Elena Dolghih, Clifford Bryant, Adam R. Renslo, Matthew P. Jacobson
2010 J jnl
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW.
PLoS Comput. Biol.
Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto López-Rendón, John Zintsmaster, Mária Ercsey-Ravasz, Christopher R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, Jesús A. Izaguirre
2007 J jnl
An atomistic model of passive membrane permeability: application to a series of FDA approved drugs.
J. Comput. Aided Mol. Des.
Chakrapani Kalyanaraman, Matthew P. Jacobson
2006 J jnl
Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation.
PLoS Comput. Biol.
Eli S. Groban, Arjun Narayanan, Matthew P. Jacobson
2006 J jnl
Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening.
J. Chem. Inf. Model.
Niu Huang, Chakrapani Kalyanaraman, John J. Irwin, Matthew P. Jacobson
2006 J jnl
What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules.
J. Comput. Chem.
Zhiyun Yu, Matthew P. Jacobson, Richard A. Friesner
2004 J jnl
A kinematic view of loop closure.
J. Comput. Chem.
Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill