A kinematic view of loop closure. - Evangelos A. Coutsias; Chaok Seok; Matthew P. Jacobson; Ken A. Dill (J. Comput. Chem., 2004)

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. - Zhiyun Yu; Matthew P. Jacobson; Richard A. Friesner (J. Comput. Chem., 2006)

Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening. - Niu Huang; Chakrapani Kalyanaraman; John J. Irwin; Matthew P. Jacobson (J. Chem. Inf. Model., 2006)

Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation. - Eli S. Groban; Arjun Narayanan; Matthew P. Jacobson (PLoS Comput. Biol., 2006)

An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. - Chakrapani Kalyanaraman; Matthew P. Jacobson (J. Comput. Aided Mol. Des., 2007)

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW. - 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 (PLoS Comput. Biol., 2010)

A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series. - Chaya Rapp; Chakrapani Kalyanaraman; Aviva Schiffmiller; Esther Leah Schoenbrun; Matthew P. Jacobson (J. Chem. Inf. Model., 2011)

A New View of the Bacterial Cytosol Environment. - Benjamin P. Cossins; Matthew P. Jacobson; Victor Guallar (PLoS Comput. Biol., 2011)

Predicting Binding to P-Glycoprotein by Flexible Receptor Docking. - Elena Dolghih; Clifford Bryant; Adam R. Renslo; Matthew P. Jacobson (PLoS Comput. Biol., 2011)

Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation. - Arjun Narayanan; Lawrence L. LeClaire III; Diane L. Barber; Matthew P. Jacobson (PLoS Comput. Biol., 2011)

Testing Physical Models of Passive Membrane Permeation. - Siegfried S. F. Leung; Jona Mijalkovic; Kenneth W. Borrelli; Matthew P. Jacobson (J. Chem. Inf. Model., 2012)

Discovery of new enzymes and metabolic pathways by using structure and genome context. - 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; et al. (Nat., 2013)

Prediction of Substrates for Glutathione Transferases by Covalent Docking. - Guang Qiang Dong; Sara Calhoun; Hao Fan 002; Chakrapani Kalyanaraman; Megan C. Branch; Susan T. Mashiyama; Nir London; Matthew P. Jacobson; Patricia C. Babbitt; Brian K. Shoichet; Richard N. Armstrong; Andrej Sali (J. Chem. Inf. Model., 2014)

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery. - Lili X. Peng; Monica T. Hsu; Massimiliano Bonomi; David A. Agard; Matthew P. Jacobson (PLoS Comput. Biol., 2014)

Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach. - Bo-Xue Tian; Frank H. Wallrapp; Gemma L. Holliday; Jeng-Yeong Chow; Patricia C. Babbitt; C. Dale Poulter; Matthew P. Jacobson (PLoS Comput. Biol., 2014)

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition. - Siegfried S. F. Leung; Daniel J. Sindhikara; Matthew P. Jacobson (J. Chem. Inf. Model., 2016)

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction. - Qin Wang 010; Simone Sciabola; Gabriela Barreiro; Xinjun Hou; Guoyun Bai; Michael J. Shapiro; Frank Koehn; Anabella Villalobos; Matthew P. Jacobson (J. Chem. Inf. Model., 2016)

Non-degradative Ubiquitination of Protein Kinases. - K. Aurelia Ball; Jeffrey R. Johnson; Mary K. Lewinski; John Guatelli; Erik Verschueren; Nevan J. Krogan; Matthew P. Jacobson (PLoS Comput. Biol., 2016)

Defining the Product Chemical Space of Monoterpenoid Synthases. - Bo-Xue Tian; C. Dale Poulter; Matthew P. Jacobson (PLoS Comput. Biol., 2016)