List of works - Matthew P. Jacobson

2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease

scientific article published on 18 March 2013

A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP.

scientific article published on 17 February 2015

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

scientific article published on 30 April 2020

A Unique cis-3-Hydroxy-l-proline Dehydratase in the Enolase Superfamily

article

A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection

scientific article published on 23 September 2013

A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

scientific article

A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion

scientific article (publication date: 2014)

A new view of the bacterial cytosol environment

scientific article

A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection

scientific article

A potent and selective inhibitor targeting human and murine 12/15-LOX.

scientific article

A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle

scientific article published on 23 February 2018

A structure-based model for predicting serum albumin binding

scientific article

Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2

scientific article

Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response

scientific article published on 09 August 2019

An atomistic model of passive membrane permeability: application to a series of FDA approved drugs

article

Antibodies as a model system for comparative model refinement.

scientific article published on August 2010

Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells.

scientific article

Assessment of protein structure refinement in CASP9.

scientific article

Assessment of the protein-structure refinement category in CASP8

scientific article

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

scientific article published on 11 July 2016

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

scientific article

Automated site preparation in physics-based rescoring of receptor ligand complexes

scientific article published on October 2009

Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products.

scientific article published on 12 June 2015

Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice

scientific article published on 21 August 2013

Binding-site assessment by virtual fragment screening

scientific article

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins

scientific article published on 5 September 2017

Cell-permeable cyclic peptides from synthetic libraries inspired by natural products.

scientific article published on 8 January 2015

Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding

scientific journal article

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion

scientific article published on 13 April 2012

Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent

scientific article

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

scientific article

Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis ,

scientific article

Computational modeling of the catalytic reaction in triosephosphate isomerase.

scientific article

Computational studies of protein regulation by post-translational phosphorylation.

scientific article

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

scientific article published on 21 April 2015

Computer-aided antibody design

scientific article

Conformational changes in protein loops and helices induced by post-translational phosphorylation

scientific article

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

scientific article published in November 2006

Conformational selection in silico: loop latching motions and ligand binding in enzymes.

scientific article

Considering protonation as a posttranslational modification regulating protein structure and function

scientific article

Defining the Product Chemical Space of Monoterpenoid Synthases

scientific article

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

scientific article published on 15 November 2012

Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.

scientific article

Designing molecules to cross biological membranes.

scientific article published in January 2013

Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen

scientific article published on 5 October 2017

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction.

scientific article

Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin.

scientific article published on 23 January 2017

Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators.

scientific article published on 18 October 2017

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

scientific article

Discovery of new enzymes and metabolic pathways by using structure and genome context

scientific article

Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2)

scientific article

Divergent evolution in enolase superfamily: strategies for assigning functions

scientific article

Dysregulated pH: a perfect storm for cancer progression.

scientific article published on 11 August 2011

Effects of somatic mutations on CDR loop flexibility during affinity maturation

scientific article published on 06 December 2010

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

scientific article

Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58

scientific journal article

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily

scientific article published on 11 May 2006

Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior

scientific article

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics

scientific article published on 22 July 2016

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

scientific article

Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70)

scientific article published on 13 July 2018

Gasdermin D pore structure reveals preferential release of mature interleukin-1

scientific article published on 21 April 2021

GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors

scientific article published on 06 September 2016

High Throughput Screen for Inhibitors of Protein-Protein Interactions in a Reconstituted Heat Shock Protein 70 (Hsp70) Complex.

scientific article published on 2 February 2018

High-resolution prediction of protein helix positions and orientations

scientific article published in May 2004

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

scientific article

Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency

scientific article

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

scientific article published on 7 May 2009

In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life.

scientific article published on January 2013

Inhibitor binding mode and allosteric regulation of Na-glucose symporters

scientific article published on 07 December 2018

Intracellular pH sensors: design principles and functional significance

scientific article published on February 2007

Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni

scientific article

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

scientific article

Modeling conformational ensembles of slow functional motions in Pin1-WW

scientific article

Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters

scientific article published on 28 January 2022

Molecular mechanics methods for predicting protein-ligand binding.

scientific article published on September 2006

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

scientific article published on August 2009

Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro

scientific article published on 24 May 2019

Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility

scientific article published in May 2008

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

scientific article published in March 2007

Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1).

scientific article

Non-degradative Ubiquitination of Protein Kinases.

scientific article

Novel human lipoxygenase inhibitors discovered using virtual screening with homology models

scientific article published in February 2006

Novel procedure for modeling ligand/receptor induced fit effects.

scientific article

Observation of Coriolis Coupling between nu(2) + 4nu(4) and 7nu(4) in Acetylene &Xtilde;(1)Sigma(+)(g) by Stimulated Emission Pumping Spectroscopy

scientific article published on 01 February 2000

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

scientific article published on 01 July 2002

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

scientific article published on October 2012

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

scientific article (publication date: 13 February 2009)

Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides.

scientific article published on 5 June 2015

Phosphorylation of the Arp2 subunit relieves auto-inhibitory interactions for Arp2/3 complex activation

scientific article

Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening

scientific article published in January 2006

Predicting Efflux Ratios and Blood-Brain Barrier Penetration from Chemical Structure: Combining Passive Permeability with Active Efflux by P-Glycoprotein ⬇️

scientific article published on December 11, 2012

Predicting and improving the membrane permeability of peptidic small molecules.

scientific article

Predicting binding to p-glycoprotein by flexible receptor docking

scientific article

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

scientific article published on 09 August 2013

Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach

scientific article

Prediction and assignment of function for a divergent N-succinyl amino acid racemase

scientific article

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

scientific article published on 11 February 2014

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

scientific article

Prediction of side-chain conformations on protein surfaces

scientific article

Prediction of substrates for glutathione transferases by covalent docking

scientific article

Probing the Electrostatic and Steric Requirements for Substrate Binding in Human Platelet-Type 12-Lipoxygenase

scientific article published on 04 January 2019

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

scientific article

Prominent features of the amino acid mutation landscape in cancer.

scientific article published on 24 August 2017

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

scientific article

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

scientific article

Role of Human 15-Lipoxygenase-2 in the Biosynthesis of the Lipoxin Intermediate, 5S,15S-diHpETE, Implicated with the Altered Positional Specificity of Human 15-Lipoxygenase-1

scientific article published on 13 October 2020

SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production

scientific article

SIRT5 regulates the mitochondrial lysine succinylome and metabolic networks

scientific journal article

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition.

scientific article

Strengths of hydrogen bonds involving phosphorylated amino acid side chains

scientific article

Structural Characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei Bound to the Antifungal Drugs Posaconazole and Fluconazole

scientific article

Structural and Kinetic Studies of a Cisplatin-modified DNA Icosamer Binding to HMG1 Domain B

scientific article published in Journal of Biological Chemistry

Structural model and functional significance of pH-dependent talin-actin binding for focal adhesion remodeling

scientific article

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

scientific article published on 7 February 2017

Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function

scientific article

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

scientific article

Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3.

scientific article published on 5 February 2013

Surfaces affect ion pairing

scientific article published in December 2005

Synthesis and Screening of α-Xylosides in Human Glioblastoma Cells

scientific article published on 14 December 2020

Synthesis and enzymatic studies of bisubstrate analogues for farnesyl diphosphate synthase.

scientific article published on 26 March 2015

Synthesis of the Ca2+-mobilizing messengers NAADP and cADPR by intracellular CD38 enzyme in the mouse heart: Role in β-adrenoceptor signaling

scientific article published on 24 May 2017

Synthetic group A streptogramin antibiotics that overcome Vat resistance

scientific article published on 23 September 2020

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

scientific article published on 14 February 2009

Testing physical models of passive membrane permeation

scientific article

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

scientific article

The Enzyme Function Initiative

scientific article

The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery

scientific article (publication date: February 2014)

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

scientific article published on August 2008

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

scientific article published on April 2008

Tryptophan 500 and arginine 707 define product and substrate active site binding in soybean lipoxygenase-1.

scientific article published in October 2004

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

scientific article

Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods

scientific article published on 16 September 2005

Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes

scientific article

pH sensing by FAK-His58 regulates focal adhesion remodeling

scientific article published on September 2013

List of works by Matthew P. Jacobson

2-Aminothiazoles with improved pharmacotherapeutic properties for treatment of prion disease

A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

A Unique cis-3-Hydroxy-l-proline Dehydratase in the Enolase Superfamily

A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection

A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion

A new view of the bacterial cytosol environment

A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection

A potent and selective inhibitor targeting human and murine 12/15-LOX.

A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle

A structure-based model for predicting serum albumin binding

Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2

Age- and stress-associated C. elegans granulins impair lysosomal function and induce a compensatory HLH-30/TFEB transcriptional response

An atomistic model of passive membrane permeability: application to a series of FDA approved drugs

Antibodies as a model system for comparative model refinement.

Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells.

Assessment of protein structure refinement in CASP9.

Assessment of the protein-structure refinement category in CASP8

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

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

Automated site preparation in physics-based rescoring of receptor ligand complexes

Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products.

Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice

Binding-site assessment by virtual fragment screening

Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins

Cell-permeable cyclic peptides from synthetic libraries inspired by natural products.

Cofilin is a pH sensor for actin free barbed end formation: role of phosphoinositide binding

Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion

Competition between intramolecular hydrogen bonds and solvation in phosphorylated peptides: simulations with explicit and implicit solvent

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Computation-Facilitated Assignment of the Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis ,

Computational modeling of the catalytic reaction in triosephosphate isomerase.

Computational studies of protein regulation by post-translational phosphorylation.

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

Computer-aided antibody design

Conformational changes in protein loops and helices induced by post-translational phosphorylation

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

Conformational selection in silico: loop latching motions and ligand binding in enzymes.

Considering protonation as a posttranslational modification regulating protein structure and function

Defining the Product Chemical Space of Monoterpenoid Synthases

Design of a phosphorylatable PDZ domain with peptide-specific affinity changes

Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis.

Designing molecules to cross biological membranes.

Development of 5N-Bicalutamide, a High-Affinity Reversible Covalent Antiandrogen

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction.

Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin.

Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators.

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

Discovery of new enzymes and metabolic pathways by using structure and genome context

Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2)

Divergent evolution in enolase superfamily: strategies for assigning functions

Dysregulated pH: a perfect storm for cancer progression.

Effects of somatic mutations on CDR loop flexibility during affinity maturation

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

Evolution of enzymatic activities in the enolase superfamily: galactarate dehydratase III from Agrobacterium tumefaciens C58

Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily

Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior

Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics

Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.

Exploration of Benzothiazole Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70)

Gasdermin D pore structure reveals preferential release of mature interleukin-1

GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors

High Throughput Screen for Inhibitors of Protein-Protein Interactions in a Reconstituted Heat Shock Protein 70 (Hsp70) Complex.

High-resolution prediction of protein helix positions and orientations

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency

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

In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life.

Inhibitor binding mode and allosteric regulation of Na-glucose symporters

Intracellular pH sensors: design principles and functional significance

Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges

Modeling conformational ensembles of slow functional motions in Pin1-WW

Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters

Molecular mechanics methods for predicting protein-ligand binding.

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

Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro

Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility