Matthew P. Jacobson

Publication Activity (10 Years)

Years Active: 2004-2016
Publications (10 Years): 4

Top Topics

Predictive Model

Sequenced Genomes

Physical Models

Metabolic Pathways

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Qin Wang, Simone Sciabola, Gabriela Barreiro, Xinjun Hou, Guoyun Bai, Michael J. Shapiro, Frank Koehn, Anabella Villalobos, Matthew P. Jacobson
Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. J. Chem. Inf. Model. 56 (11) (2016)
K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson
Non-degradative Ubiquitination of Protein Kinases. PLoS Comput. Biol. 12 (6) (2016)
Bo-Xue Tian, C. Dale Poulter, Matthew P. Jacobson
Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput. Biol. 12 (8) (2016)
Siegfried S. F. Leung, Daniel J. Sindhikara, Matthew P. Jacobson
Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. J. Chem. Inf. Model. 56 (5) (2016)
Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach. PLoS Comput. Biol. 10 (10) (2014)
Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson
The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery. PLoS Comput. Biol. 10 (2) (2014)
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
Prediction of Substrates for Glutathione Transferases by Covalent Docking. J. Chem. Inf. Model. 54 (6) (2014)
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
Discovery of new enzymes and metabolic pathways by using structure and genome context. Nat. 502 (7473) (2013)
Siegfried S. F. Leung, Jona Mijalkovic, Kenneth W. Borrelli, Matthew P. Jacobson
Testing Physical Models of Passive Membrane Permeation. J. Chem. Inf. Model. 52 (6) (2012)
Benjamin P. Cossins, Matthew P. Jacobson, Victor Guallar
A New View of the Bacterial Cytosol Environment. PLoS Comput. Biol. 7 (6) (2011)
Chaya Rapp, Chakrapani Kalyanaraman, Aviva Schiffmiller, Esther Leah Schoenbrun, Matthew P. Jacobson
A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series. J. Chem. Inf. Model. 51 (9) (2011)
Elena Dolghih, Clifford Bryant, Adam R. Renslo, Matthew P. Jacobson
Predicting Binding to P-Glycoprotein by Flexible Receptor Docking. PLoS Comput. Biol. 7 (6) (2011)
Arjun Narayanan, Lawrence L. LeClaire III, Diane L. Barber, Matthew P. Jacobson
Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation. PLoS Comput. Biol. 7 (11) (2011)
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
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW. PLoS Comput. Biol. 6 (12) (2010)
Chakrapani Kalyanaraman, Matthew P. Jacobson
An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J. Comput. Aided Mol. Des. 21 (12) (2007)
Zhiyun Yu, Matthew P. Jacobson, Richard A. Friesner
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. 27 (1) (2006)
Eli S. Groban, Arjun Narayanan, Matthew P. Jacobson
Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation. PLoS Comput. Biol. 2 (4) (2006)
Niu Huang, Chakrapani Kalyanaraman, John J. Irwin, Matthew P. Jacobson
Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening. J. Chem. Inf. Model. 46 (1) (2006)
Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill
A kinematic view of loop closure. J. Comput. Chem. 25 (4) (2004)