Matthew P Jacobson

发表

Toward better refinement of comparative models: Predicting loops in inexact environments

Kai Zhu, Richard A Friesner, Benjamin D. Sellers, 2008, Proteins.

Assessing protein loop flexibility by hierarchical Monte Carlo sampling.

Jerome Nilmeier, Matthew P Jacobson, Evangelos A Coutsias, 2011, Journal of chemical theory and computation.

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.

Matthew P Jacobson, Katrina W Lexa, Sara N Pollock, 2016, Journal of chemical theory and computation.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Prediction of enzymatic pathways by integrative pathway mapping

Henry Lin, Andrej Sali, Matthew P Jacobson, 2018, eLife.

Antibodies as a model system for comparative model refinement

Benjamin D. Sellers, Benjamin D Sellers, Matthew P Jacobson, 2010, Proteins.

Assessment of protein structure refinement in CASP9

Matthew P Jacobson, Ken A Dill, Justin L MacCallum, 2011, Proteins.

Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo.

Jerome Nilmeier, Matthew P Jacobson, 2009, Journal of chemical theory and computation.

Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes.

Kai Zhu, Richard A Friesner, Matthew P Jacobson, 2007, Journal of chemical theory and computation.

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.

Matthew P Jacobson, Christopher L. McClendon, Lan Hua, 2012, Journal of chemical theory and computation.

Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products.

Matthew P Jacobson, Katrina W Lexa, Katrina W. Lexa, 2015, Journal of medicinal chemistry.

Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling

Xin Li, Richard A Friesner, Matthew P Jacobson, 2006, Proteins.

Effects of somatic mutations on CDR loop flexibility during affinity maturation

Benjamin D. Sellers, Matthew P Jacobson, Sergio E Wong, 2011, Proteins.

Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains.

Benjamin D. Sellers, Benjamin D Sellers, Matthew P Jacobson, 2009, Journal of molecular biology.

Considering protonation as a posttranslational modification regulating protein structure and function.

Matthew P Jacobson, D. Barber, M. Jacobson, 2013, Annual review of biophysics.

Conformational selection in silico: Loop latching motions and ligand binding in enzymes

Matthew P Jacobson, Sergio E. Wong, Sergio Wong, 2008, Proteins.

Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers.

Matthew P Jacobson, R Scott Lokey, Taha Rezai, 2006, Journal of the American Chemical Society.

Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.

Heidi J Imker, Matthew P Jacobson, Heidi J. Imker, 2008, Structure.

Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

Eyal Akiva, Matthew P Jacobson, Suwen Zhao, 2014, eLife.

Turning a protein kinase on or off from a single allosteric site via disulfide trapping

Matthew P Jacobson, Christopher L. McClendon, Dennis W Wolan, 2011, Proceedings of the National Academy of Sciences.

Computational studies of protein regulation by post-translational phosphorylation.

Matthew P Jacobson, Arjun Narayanan, M. Jacobson, 2009, Current opinion in structural biology.

Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides.

Matthew P Jacobson, Chakrapani Kalyanaraman, R Scott Lokey, 2006, Journal of the American Chemical Society.

Physics-based methods for studying protein-ligand interactions.

Niu Huang, Matthew P Jacobson, M. Jacobson, 2007, Current opinion in drug discovery & development.

Biaryl Amides and Hydrazones as Therapeutics for Prion Disease in Transgenic Mice

Zhe Li, Matthew P Jacobson, Adam R Renslo, 2013, The Journal of Pharmacology and Experimental Therapeutics.

Studying enzyme-substrate specificity in silico: a case study of the Escherichia coli glycolysis pathway.

Matthew P Jacobson, Chakrapani Kalyanaraman, M. Jacobson, 2010, Biochemistry.

Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.

Matthew P Jacobson, Katrina W Lexa, Katrina W. Lexa, 2017, Journal of the American Chemical Society.

Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein.

Matthew P Jacobson, Elena Dolghih, M. Jacobson, 2013, ACS chemical neuroscience.

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.

David L Mobley, Matthew P Jacobson, Gregory Friedland, 2009, Journal of chemical theory and computation.

Toward deciphering the code to aminergic G protein-coupled receptor drug design.

Matthew P Jacobson, Eli S Groban, Eli S. Groban, 2008, Chemistry & biology.

Predicting enzyme-substrate specificity with QM/MM methods: a case study of the stereospecificity of (D)-glucarate dehydratase.

Matthew P Jacobson, Suwen Zhao, Chakrapani Kalyanaraman, 2013, Biochemistry.

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

Matthew P Jacobson, Suwen Zhao, Brian San Francisco, 2016, Proceedings of the National Academy of Sciences.

Improving the species cross-reactivity of an antibody using computational design.

Benjamin D. Sellers, Benjamin D Sellers, Matthew P Jacobson, 2009, Bioorganic & medicinal chemistry letters.

Surfaces affect ion pairing.

Matthew P Jacobson, Ken A Dill, Ilya Chorny, 2005, The journal of physical chemistry. B.

Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods

Matthew P Jacobson, Chakrapani Kalyanaraman, M. Jacobson, 2005, Journal of biomolecular screening.

Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance().

Yizhong Zhang, Matthew P Jacobson, Spiros Liras, 2012, MedChemComm.

Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis .

Matthew P Jacobson, Chakrapani Kalyanaraman, Stephen K Burley, 2009, Biochemistry.