Search Results - "Duca JS"

Discovery of EGT710, an Oral Nonpeptidomimetic Reversible Covalent SARS-CoV-2 Main Protease Inhibitor.

Authors: Papillon JPN Yuan J Hesse MJ et al.

Source: Journal of medicinal chemistry [J Med Chem] 2026 Feb 26; Vol. 69 (4), pp. 3868-3886. Date of Electronic Publication: 2026 Feb 09.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 9716531 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-4804 (Electronic) Linking ISSN: 00222623 NLM ISO Abbreviation: J Med Chem Subsets: MEDLINE

The current understanding of KRAS oligomerization on membranes.

Authors: Lesgidou N Papadourakis M Mandal N et al.

Source: Current opinion in structural biology [Curr Opin Struct Biol] 2026 Feb; Vol. 96, pp. 103190. Date of Electronic Publication: 2025 Dec 12.

Publication Type: Journal Article; Review

Journal Info: Publisher: Elsevier Science Country of Publication: England NLM ID: 9107784 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-033X (Electronic) Linking ISSN: 0959440X NLM ISO Abbreviation: Curr Opin Struct Biol Subsets: MEDLINE

Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design.

Authors: Danilack AD Dickson CJ Soylu C et al.

Source: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2024 May 01; Vol. 38 (1), pp. 21. Date of Electronic Publication: 2024 May 01.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Springer Country of Publication: Netherlands NLM ID: 8710425 Publication Model: Electronic Cited Medium: Internet ISSN: 1573-4951 (Electronic) Linking ISSN: 0920654X NLM ISO Abbreviation: J Comput Aided Mol Des Subsets: MEDLINE

Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications.

Authors: Koukos PI Dehghani-Ghahnaviyeh S Velez-Vega C et al.

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2023 Dec 12; Vol. 19 (23), pp. 8901-8918. Date of Electronic Publication: 2023 Nov 29.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening.

Authors: Chen L Cruz A Ramsey S et al.

Source: PloS one [PLoS One] 2019 Aug 20; Vol. 14 (8), pp. e0220113. Date of Electronic Publication: 2019 Aug 20 (Print Publication: 2019).

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability.

Authors: Andreadelis I Kiriakidi S Lamprakis C et al.

Source: The journal of physical chemistry. B [J Phys Chem B] 2022 Feb 24; Vol. 126 (7), pp. 1504-1519. Date of Electronic Publication: 2022 Feb 10.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101157530 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5207 (Electronic) Linking ISSN: 15205207 NLM ISO Abbreviation: J Phys Chem B Subsets: MEDLINE

Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots.

Authors: Dickson CJ Hornak V Duca JS

Source: Journal of chemical information and modeling [J Chem Inf Model] 2021 Dec 27; Vol. 61 (12), pp. 5923-5930. Date of Electronic Publication: 2021 Nov 29.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.

Authors: Sherborne B Shanmugasundaram V Cheng AC et al.

Source: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2016 Dec; Vol. 30 (12), pp. 1139-1141. Date of Electronic Publication: 2016 Dec 24.

Publication Type: Conference Proceedings

Journal Info: Publisher: Springer Country of Publication: Netherlands NLM ID: 8710425 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-4951 (Electronic) Linking ISSN: 0920654X NLM ISO Abbreviation: J Comput Aided Mol Des Subsets: MEDLINE

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments.

Authors: Lamprakis C Andreadelis I Manchester J et al.

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2021 May 11; Vol. 17 (5), pp. 3088-3102. Date of Electronic Publication: 2021 Apr 29.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.

Authors: Pavlova A Lynch DL Daidone I et al.

Source: Chemical science [Chem Sci] 2020 Nov 26; Vol. 12 (4), pp. 1513-1527. Date of Electronic Publication: 2020 Nov 26 (Print Publication: 2021).

Publication Type: Journal Article

Journal Info: Publisher: Royal Society of Chemistry Country of Publication: England NLM ID: 101545951 Publication Model: eCollection Cited Medium: Print ISSN: 2041-6520 (Print) Linking ISSN: 20416520 NLM ISO Abbreviation: Chem Sci Subsets: PubMed not MEDLINE

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.

Authors: Pavlova A Lynch DL Daidone I et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2020 Sep 10. Date of Electronic Publication: 2020 Sep 10.

Publication Type: Preprint; Journal Article

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

Rethinking drug design in the artificial intelligence era.

Authors: Schneider P Walters WP Plowright AT et al.

Source: Nature reviews. Drug discovery [Nat Rev Drug Discov] 2020 May; Vol. 19 (5), pp. 353-364. Date of Electronic Publication: 2019 Dec 04.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101124171 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1474-1784 (Electronic) Linking ISSN: 14741776 NLM ISO Abbreviation: Nat Rev Drug Discov Subsets: MEDLINE

Revealing Molecular Determinants of hERG Blocker and Activator Binding.

Authors: Dickson CJ Velez-Vega C Duca JS

Source: Journal of chemical information and modeling [J Chem Inf Model] 2020 Jan 27; Vol. 60 (1), pp. 192-203. Date of Electronic Publication: 2020 Jan 10.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts.

Authors: Lesburg CA Duca JS

Source: Nucleic acids research [Nucleic Acids Res] 2008 Jul 01; Vol. 36 (Web Server issue), pp. W252-4. Date of Electronic Publication: 2008 May 16.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Using Membrane Partitioning Simulations To Predict Permeability of Forty-Nine Drug-Like Molecules.

Authors: Dickson CJ Hornak V Bednarczyk D et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2019 Jan 28; Vol. 59 (1), pp. 236-244. Date of Electronic Publication: 2018 Dec 26.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

Structure-Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling.

Authors: Dickson CJ Hornak V Pearlstein RA et al.

Source: Journal of the American Chemical Society [J Am Chem Soc] 2017 Jan 11; Vol. 139 (1), pp. 442-452. Date of Electronic Publication: 2016 Dec 21.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 7503056 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5126 (Electronic) Linking ISSN: 00027863 NLM ISO Abbreviation: J Am Chem Soc Subsets: MEDLINE

Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding.

Authors: Dickson CJ Hornak V Velez-Vega C et al.

Source: Journal of medicinal chemistry [J Med Chem] 2016 Jun 23; Vol. 59 (12), pp. 5780-9. Date of Electronic Publication: 2016 Jun 07.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 9716531 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-4804 (Electronic) Linking ISSN: 00222623 NLM ISO Abbreviation: J Med Chem Subsets: MEDLINE

Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation.

Authors: Pearlstein RA MacCannell KA Erdemli G et al.

Source: Current topics in medicinal chemistry [Curr Top Med Chem] 2016; Vol. 16 (16), pp. 1792-818.

Publication Type: Journal Article; Review

Journal Info: Publisher: Bentham Science Publishers Country of Publication: United Arab Emirates NLM ID: 101119673 Publication Model: Print Cited Medium: Internet ISSN: 1873-4294 (Electronic) Linking ISSN: 15680266 NLM ISO Abbreviation: Curr Top Med Chem Subsets: MEDLINE

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

Authors: Velez-Vega C McKay DJ Kurtzman T et al.

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2015 Nov 10; Vol. 11 (11), pp. 5090-102. Date of Electronic Publication: 2015 Oct 21.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE

Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH.

Authors: Velez-Vega C McKay DJ Aravamuthan V et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2014 Dec 22; Vol. 54 (12), pp. 3344-61. Date of Electronic Publication: 2014 Nov 26.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE