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2010 – 2019
- 2016
[j19]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): 924-929 (2016)- [j18]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): 2194-2206 (2016) - [j17]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) - [j16]Bo-Xue Tian, C. Dale Poulter, Matthew P. Jacobson:
Defining the Product Chemical Space of Monoterpenoid Synthases. PLoS Comput. Biol. 12(8) (2016) - 2014
- [j15]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): 1687-1699 (2014) - [j14]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) - [j13]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) - 2013
- [j12]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): 698-702 (2013) - 2012
- [j11]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): 1621-1636 (2012) - 2011
- [j10]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): 2082-2089 (2011) - [j9]Benjamin P. Cossins, Matthew P. Jacobson, Victor Guallar:
A New View of the Bacterial Cytosol Environment. PLoS Comput. Biol. 7(6) (2011) - [j8]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) - [j7]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) - 2010
- [j6]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)
2000 – 2009
- 2007
- [j5]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): 675-679 (2007) - 2006
- [j4]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): 72-89 (2006) - [j3]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): 243-253 (2006) - [j2]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) - 2004
- [j1]Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill:
A kinematic view of loop closure. J. Comput. Chem. 25(4): 510-528 (2004)
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