D. Joseph-McCarthy

发表

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Alexander D. MacKerell, M. Karplus, D. Nguyen, 1998, The journal of physical chemistry. B.

Computational approaches to structure-based ligand design.

D. Joseph-McCarthy, 1999, Pharmacology & therapeutics.

The specter of Manaus: the risks of a rapid return to pre-pandemic conditions after COVID-19 vaccine rollout

D. Joseph-McCarthy, A. Chakravarty, D. Van Egeren, 2021, medRxiv.

Pharmacophore-Based Molecular Docking: A Practical Guide

D. Joseph-McCarthy, J. Alvarez, J. Zou, 2005 .

Structure-based optimization of protein tyrosine phosphatase 1B inhibitors: from the active site to the second phosphotyrosine binding site.

A. Moretto, D. Joseph-McCarthy, T. Mansour, 2007, Journal of medicinal chemistry.

An Antipersister Strategy for Treatment of Chronic Pseudomonas aeruginosa Infections

F. Ausubel, M. Koeva, D. Joseph-McCarthy, 2017, Antimicrobial Agents and Chemotherapy.

Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs

M Karplus, M. Karplus, D. Joseph-McCarthy, 1997, Proteins.

Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein

D. Joseph-McCarthy, J. Carlson, A. Chakravarty, 2020, medRxiv.

Identification and characterization of acidic mammalian chitinase inhibitors.

D. Joseph-McCarthy, J. Ellingboe, Jaison Jacob, 2010, Journal of medicinal chemistry.

Design and synthesis of 3,3-piperidine hydroxamate analogs as selective TACE inhibitors.

D. Joseph-McCarthy, J. Levin, E. Feyfant, 2007, Bioorganic & medicinal chemistry letters.

Carbonic Anhydrase-Inhibitor Binding: From Solution to the Gas Phase

Richard D. Smith, G. Whitesides, D. Joseph-McCarthy, 1997 .

Vaccines Alone Cannot Slow the Evolution of SARS-CoV-2

D. Joseph-McCarthy, A. Chakravarty, N. Hochberg, 2022, medRxiv.

Rapid relaxation of pandemic restrictions after vaccine rollout favors growth of SARS-CoV-2 variants: A model-based analysis

D. Joseph-McCarthy, A. Chakravarty, M. S. Rogers, 2021, PloS one.

1,2,4-Oxadiazolidin-3,5-diones and 1,3,5-triazin-2,4,6-triones as cytosolic phospholipase A2α inhibitors

D. Joseph-McCarthy, J. McKew, A. Gopalsamy, 2006 .

Structure–activity relationships of indole cytosolic phospholipase A2α inhibitors: substrate mimetics

J. Alvarez, D. Joseph-McCarthy, J. D. Clark, 2003 .

Bicyclic and tricyclic thiophenes as protein tyrosine phosphatase 1B inhibitors.

A. Moretto, D. Joseph-McCarthy, D. P. Wilson, 2006, Bioorganic & medicinal chemistry.

Probing acid replacements of thiophene PTP1B inhibitors.

D. Joseph-McCarthy, M. Tam, Weixin Xu, 2007, Bioorganic & medicinal chemistry letters.

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Stuart L. Schreiber, Gregory A. Weiss, Erik Evensen, 2007, J. Comput. Aided Mol. Des..

A structurally biased combinatorial approach for discovering new anti-picornaviral compounds.

G. Whitesides, D. Joseph-McCarthy, L. Isaacs, 2001, Chemistry & biology.

No magic bullet: Limiting in-school transmission in the face of variable SARS-CoV-2 viral loads

D. Joseph-McCarthy, A. Chakravarty, N. Hochberg, 2022, Frontiers in Public Health.

Catalytic Domain Crystal Structure of Protein Kinase C-θ (PKCθ)*♦

Rita Greco, Diane Joseph-McCarthy, L. Mosyak, 2004, Journal of Biological Chemistry.

Automated generation of MCSS‐derived pharmacophoric DOCK site points for searching multiconformation databases

D. Joseph-McCarthy, J. Alvarez, Diane Joseph‐McCarthy, 2003, Proteins.

Endemicity is not a victory: the unmitigated downside risks of widespread SARS-CoV-2 transmission

D. Joseph-McCarthy, N. Hochberg, L. White, 2022, medRxiv.

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

D. Joseph-McCarthy, J. Carlson, A. Chakravarty, 2021, PloS one.

Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure

D. Joseph-McCarthy, A. Chakravarty, M. S. Rogers, 2021, Scientific Reports.

Controlling long-term SARS-CoV-2 infections is important for slowing viral evolution

D. Joseph-McCarthy, A. Chakravarty, D. Van Egeren, 2021, medRxiv.

Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid.

G. Petsko, E. Komives, D. Joseph-McCarthy, 1994, Biochemistry.

Inhibitors of tumor progression loci-2 (Tpl2) kinase and tumor necrosis factor alpha (TNF-alpha) production: selectivity and in vivo antiinflammatory activity of novel 8-substituted-4-anilino-6-aminoquinoline-3-carbonitriles.

D. Joseph-McCarthy, J. Telliez, J. Cuozzo, 2007, Journal of medicinal chemistry.

Anthranilate 4H-oxazol-5-ones: novel small molecule antibacterial acyl carrier protein synthase (AcpS) inhibitors.

D. Joseph-McCarthy, C. Fritz, I. McFadyen, 2004, Bioorganic & medicinal chemistry letters.

Triad of polar residues implicated in pH specificity of acidic mammalian chitinase

L. Mosyak, D. Joseph-McCarthy, W. Somers, 2009, Protein science : a publication of the Protein Society.

In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound.

Diane Joseph-McCarthy, Sameer Kawatkar, D. Joseph-McCarthy, 2012, ACS chemical biology.

Fragment-Based Lead Discovery and Design

Diane Joseph-McCarthy, Demetri Moustakas, Arthur J. Campbell, 2014, J. Chem. Inf. Model..

Discovery of selective and potent inhibitors of gram-positive bacterial thymidylate kinase (TMK).

Diane Joseph-McCarthy, Jon Read, Sameer Kawatkar, 2012, Journal of medicinal chemistry.

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

Hongming Wang, Diane Joseph-McCarthy, Sameer Kawatkar, 2009, J. Comput. Aided Mol. Des..

Ensemble-Based Docking Using Biased Molecular Dynamics

Diane Joseph-McCarthy, Michelle L. Lamb, Arthur J. Campbell, 2014, J. Chem. Inf. Model..

Investigation of MM-PBSA Rescoring of Docking Poses

Christine Humblet, Diane Joseph-McCarthy, David C. Thompson, 2008, J. Chem. Inf. Model..

Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design.

A. Fedorov, S. Almo, D. Joseph-McCarthy, 1996, Protein engineering.

CONFIRM: connecting fragments found in receptor molecules

Ramaswamy Nilakantan, R. Aldrin Denny, Christine Humblet, 2008, J. Comput. Aided Mol. Des..

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP

Demetri T. Moustakas, Diane Joseph-McCarthy, Michelle L. Lamb, 2015, J. Chem. Inf. Model..

Use of structure-based drug design approaches to obtain novel anthranilic acid acyl carrier protein synthase inhibitors.

Dominick Quagliato, Diane Joseph-McCarthy, Elena Severina, 2005, Journal of medicinal chemistry.

Machine learning for the identification of respiratory viral attachment machinery from sequences data

D. Joseph-McCarthy, A. Chakravarty, Kenji C Walker, 2023, PloS one.

On a model-based approach to improve intranasal spray targeting for respiratory viral infections

D. Joseph-McCarthy, A. Chakravarty, A. Mituniewicz, 2023, Frontiers in Drug Delivery.

A model-based approach to improve intranasal sprays for respiratory viral infections

D. Joseph-McCarthy, A. Mituniewicz, J. Suman, 2022, medRxiv.

From SARS-CoV-2 infection to COVID-19 morbidity: an in silico projection of virion flow rates to the lower airway via nasopharyngeal fluid boluses

D. Joseph-McCarthy, N. Hochberg, B. Senior, 2022, Rhinology Online.

Virtual fragment screening: exploration of MM-PBSA re-scoring

Matthew Miller, Diane Joseph-McCarthy, Sameer Kawatkar, 2012, Journal of Computer-Aided Molecular Design.

Ganglioside Inhibition of Neurite Outgrowth Requires Nogo Receptor Function

M. Pangalos, D. Joseph-McCarthy, Gareth Williams, 2008, Journal of Biological Chemistry.

Identification of potent and selective TACE inhibitors via the S1 pocket.

Diane Joseph-McCarthy, Linhong Sun, D. Joseph-McCarthy, 2007, Bioorganic & medicinal chemistry letters.

Machine Learning for the Identification of Viral Attachment Machinery from Respiratory Virus Sequences

D. Joseph-McCarthy, A. Chakravarty, S. Demidkin, 2022, bioRxiv.

Ionic interactions in crystalline bovine pancreatic ribonuclease A.

A. Fedorov, E. Fedorov, S. Almo, 1996, Biochemistry.

Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose.

J. R. Somoza, D. Joseph-McCarthy, W. Somers, 2000, Structure.

Use of MCSS to design small targeted libraries: application to picornavirus ligands.

M Karplus, M. Karplus, D. Filman, 2001, Journal of the American Chemical Society.

Structure‐Based Optimization of Protein Tyrosine Phosphatase‐1 B Inhibitors: Capturing Interactions with Arginine 24

Wei Li, A. Moretto, D. Joseph-McCarthy, 2008, ChemMedChem.

Monocyclic thiophenes as protein tyrosine phosphatase 1B inhibitors: capturing interactions with Asp48.

D. Joseph-McCarthy, Weixin Xu, Zhao‐Kui Wan, 2006, Bioorganic & medicinal chemistry letters.

Chapter 12 Structure-Based Lead Optimization

Diane Joseph-McCarthy, D. Joseph-McCarthy, 2005 .

Pharmacophore‐based molecular docking to account for ligand flexibility

Diane Joseph-McCarthy, Demetri Moustakas, Bert E Thomas, 2003, Proteins.

Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site.

G. Petsko, E. Komives, D. Joseph-McCarthy, 1994, Biochemistry.

Structure-based optimization of PKCθ inhibitors

L. Mosyak, D. Joseph-McCarthy, W. Somers, 2007 .

Identification, characterization and initial hit-to-lead optimization of a series of 4-arylamino-3-pyridinecarbonitrile as protein kinase C theta (PKCtheta) inhibitors.

D. Joseph-McCarthy, A. Wissner, J. Ellingboe, 2008, Journal of medicinal chemistry.

Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization

James M. Hogle, Carl D. Elkin, Harmon J. Zuccola, 2000, J. Comput. Aided Mol. Des..

Structure-based optimization of PKCtheta inhibitors.

L. Mosyak, D. Joseph-McCarthy, W. Somers, 2007, Biochemical Society Transactions.

Structure-based design of TACE selective inhibitors: manipulations in the S1'-S3' pocket.

Diane Joseph-McCarthy, Linhong Sun, D. Joseph-McCarthy, 2007, Bioorganic & medicinal chemistry.

Peroxisomes, Refsum's disease and the α- and ω-oxidation of phytanic acid

J. Trimmer, M. Bootman, M. Taussig, 2007 .

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP

Alexander S. Bayden, D. Joseph-McCarthy, M. Lamb, 2015, J. Chem. Inf. Model..

Investigation of MM-PBSA Rescoring of Docking Poses

David C. Thompson, C. Humblet, D. Joseph-McCarthy, 2008, J. Chem. Inf. Model..