Matthew Jacobson
Matthew Jacobson
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Novel procedure for modeling ligand/receptor induced fit effects
W Sherman, T Day, MP Jacobson, RA Friesner, R Farid
Journal of medicinal chemistry 49 (2), 534-553, 2006
A hierarchical approach to all‐atom protein loop prediction
MP Jacobson, DL Pincus, CS Rapp, TJF Day, B Honig, DE Shaw, ...
Proteins: Structure, Function, and Bioinformatics 55 (2), 351-367, 2004
Dysregulated pH: a perfect storm for cancer progression
BA Webb, M Chimenti, MP Jacobson, DL Barber
Nature Reviews Cancer 11 (9), 671-677, 2011
On the role of the crystal environment in determining protein side-chain conformations
MP Jacobson, RA Friesner, Z Xiang, B Honig
Journal of molecular biology 320 (3), 597-608, 2002
SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production
T Shimazu, MD Hirschey, L Hua, KE Dittenhafer-Reed, B Schwer, ...
Cell metabolism 12 (6), 654-661, 2010
Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers
T Rezai, B Yu, GL Millhauser, MP Jacobson, RS Lokey
Journal of the American Chemical Society 128 (8), 2510-2511, 2006
SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks
MJ Rardin, W He, Y Nishida, JC Newman, C Carrico, SR Danielson, ...
Cell metabolism 18 (6), 920-933, 2013
Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides
T Rezai, JE Bock, MV Zhou, C Kalyanaraman, RS Lokey, MP Jacobson
Journal of the American Chemical Society 128 (43), 14073-14080, 2006
On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds
TR White, CM Renzelman, AC Rand, T Rezai, CM McEwen, VM Gelev, ...
Nature chemical biology 7 (11), 810-817, 2011
A kinematic view of loop closure
EA Coutsias, C Seok, MP Jacobson, KA Dill
Journal of computational chemistry 25 (4), 510-528, 2004
Intracellular pH sensors: design principles and functional significance
J Srivastava, DL Barber, MP Jacobson
Physiology, 2007
Computer-aided antibody design
D Kuroda, H Shirai, MP Jacobson, H Nakamura
Protein engineering, design & selection 25 (10), 507-522, 2012
Force field validation using protein side chain prediction
MP Jacobson, GA Kaminski, RA Friesner, CS Rapp
The Journal of Physical Chemistry B 106 (44), 11673-11680, 2002
Rescoring docking hit lists for model cavity sites: predictions and experimental testing
AP Graves, DM Shivakumar, SE Boyce, MP Jacobson, DA Case, ...
Journal of molecular biology 377 (3), 914-934, 2008
Quantifying correlations between allosteric sites in thermodynamic ensembles
CL McClendon, G Friedland, DL Mobley, H Amirkhani, MP Jacobson
Journal of chemical theory and computation 5 (9), 2486-2502, 2009
Molecular mechanics methods for predicting protein–ligand binding
N Huang, C Kalyanaraman, K Bernacki, MP Jacobson
Physical Chemistry Chemical Physics 8 (44), 5166-5177, 2006
Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding
C Frantz, G Barreiro, L Dominguez, X Chen, R Eddy, J Condeelis, ...
The Journal of cell biology 183 (5), 865-879, 2008
Conformational changes in protein loops and helices induced by post-translational phosphorylation
ES Groban, A Narayanan, MP Jacobson
PLoS Comput Biol 2 (4), e32, 2006
Baseline subtraction using robust local regression estimation
AF Ruckstuhl, MP Jacobson, RW Field, JA Dodd
Journal of Quantitative Spectroscopy and Radiative Transfer 68 (2), 179-193, 2001
Physics-based scoring of protein− ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
N Huang, C Kalyanaraman, JJ Irwin, MP Jacobson
Journal of chemical information and modeling 46 (1), 243-253, 2006
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