Search Results - "Tirado-Rives J"

Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors.

Authors: Czyzyk, D.J. Valhondo, M. Deiana, L. et al.

Source: European Journal of Medicinal Chemistry. Dec2019, Vol. 183, pN.PAG-N.PAG. 1p.

Free Energies of Solvation in Cyclohexane and Water: United-Atom vs All-Atom.

Authors: Jorgensen WL Tirado-Rives J

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2026 Jul 23. Date of Electronic Publication: 2026 Jul 23.

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

Polycyclic Aromatic Hydrocarbons: Solvation, Solubility, and Hydrophobic Effects from Monte Carlo Simulations.

Authors: Jorgensen WL Tirado-Rives J

Source: The journal of physical chemistry. B [J Phys Chem B] 2025 Oct 09; Vol. 129 (40), pp. 10467-10477. Date of Electronic Publication: 2025 Sep 25.

Publication Type: Journal Article

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; PubMed not MEDLINE

Free Energies of Solvation in Benzene and Hexafluorobenzene: Is Explicit Polarization Needed?

Authors: Jorgensen WL Tirado-Rives J

Source: The journal of physical chemistry. B [J Phys Chem B] 2025 Jul 03; Vol. 129 (26), pp. 6574-6583. Date of Electronic Publication: 2025 Jun 18.

Publication Type: Journal Article

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; PubMed not MEDLINE

The need to implement FAIR principles in biomolecular simulations.

Authors: Amaro RE Åqvist J Bahar I et al.

Source: Nature methods [Nat Methods] 2025 Apr; Vol. 22 (4), pp. 641-645.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE; In Process

OPLS/2020 Force Field for Unsaturated Hydrocarbons, Alcohols, and Ethers.

Authors: Jorgensen WL Ghahremanpour MM Saar A et al.

Source: The journal of physical chemistry. B [J Phys Chem B] 2024 Jan 11; Vol. 128 (1), pp. 250-262. Date of Electronic Publication: 2023 Dec 21.

Publication Type: Journal Article

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; PubMed not MEDLINE

Ensemble Geometric Deep Learning of Aqueous Solubility.

Authors: Ghahremanpour MM Saar A Tirado-Rives J et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2023 Dec 11; Vol. 63 (23), pp. 7338-7349. Date of Electronic Publication: 2023 Nov 21.

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

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

Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors.

Authors: Saar A Ghahremanpour MM Tirado-Rives J et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2023 Nov 27; Vol. 63 (22), pp. 7210-7218. Date of Electronic Publication: 2023 Nov 07.

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

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

Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease.

Authors: Ghahremanpour MM Saar A Tirado-Rives J et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2023 Aug 28; Vol. 63 (16), pp. 5309-5318. Date of Electronic Publication: 2023 Aug 10.

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

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

Refinement of the Optimized Potentials for Liquid Simulations Force Field for Thermodynamics and Dynamics of Liquid Alkanes.

Authors: Ghahremanpour MM Tirado-Rives J Jorgensen WL

Source: The journal of physical chemistry. B [J Phys Chem B] 2022 Aug 11; Vol. 126 (31), pp. 5896-5907. Date of Electronic Publication: 2022 Aug 01.

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

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

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands.

Authors: Dodda LS Cabeza de Vaca I Tirado-Rives J et al.

Source: Nucleic acids research [Nucleic Acids Res] 2017 Jul 03; Vol. 45 (W1), pp. W331-W336.

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

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

Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency.

Authors: Zhang CH Spasov KA Reilly RA et al.

Source: ACS medicinal chemistry letters [ACS Med Chem Lett] 2021 Jul 14; Vol. 12 (8), pp. 1325-1332. Date of Electronic Publication: 2021 Jul 14 (Print Publication: 2021).

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101521073 Publication Model: eCollection Cited Medium: Print ISSN: 1948-5875 (Print) Linking ISSN: 19485875 NLM ISO Abbreviation: ACS Med Chem Lett Subsets: PubMed not MEDLINE

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.

Authors: Zhang CH Stone EA Deshmukh M et al.

Source: ACS central science [ACS Cent Sci] 2021 Mar 24; Vol. 7 (3), pp. 467-475. Date of Electronic Publication: 2021 Feb 22.

Publication Type: Journal Article

Journal Info: Publisher: ACS Publications Country of Publication: United States NLM ID: 101660035 Publication Model: Print-Electronic Cited Medium: Print ISSN: 2374-7943 (Print) Linking ISSN: 23747943 NLM ISO Abbreviation: ACS Cent Sci Subsets: PubMed not MEDLINE

Explicit Representation of Cation-π Interactions in Force Fields with 1/r⁴ Nonbonded Terms.

Authors: Turupcu A Tirado-Rives J Jorgensen WL

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2020 Nov 10; Vol. 16 (11), pp. 7184-7194. Date of Electronic Publication: 2020 Oct 13.

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

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2.

Authors: Ghahremanpour MM Tirado-Rives J Deshmukh M et al.

Source: ACS medicinal chemistry letters [ACS Med Chem Lett] 2020 Oct 25; Vol. 11 (12), pp. 2526-2533. Date of Electronic Publication: 2020 Oct 25 (Print Publication: 2020).

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101521073 Publication Model: eCollection Cited Medium: Print ISSN: 1948-5875 (Print) Linking ISSN: 19485875 NLM ISO Abbreviation: ACS Med Chem Lett Subsets: PubMed not MEDLINE

Metadynamics as a Postprocessing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2.

Authors: Cutrona KJ Newton AS Krimmer SG et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2020 Sep 28; Vol. 60 (9), pp. 4403-4415. Date of Electronic Publication: 2020 May 27.

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

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor.

Authors: Qian Y Cabeza de Vaca I Vilseck JZ et al.

Source: The journal of physical chemistry. B [J Phys Chem B] 2019 Oct 17; Vol. 123 (41), pp. 8675-8685. Date of Electronic Publication: 2019 Oct 07.

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

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

QM/MM Calculations for the Cl^- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory.

Authors: Tirado-Rives J Jorgensen WL

Source: The journal of physical chemistry. A [J Phys Chem A] 2019 Jul 11; Vol. 123 (27), pp. 5713-5717. Date of Electronic Publication: 2019 Jun 27.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 9890903 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5215 (Electronic) Linking ISSN: 10895639 NLM ISO Abbreviation: J Phys Chem A Subsets: PubMed not MEDLINE

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution.

Authors: Cabeza de Vaca I Zarzuela R Tirado-Rives J et al.

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2019 Jul 09; Vol. 15 (7), pp. 3941-3948. Date of Electronic Publication: 2019 Jun 24.

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: PubMed not MEDLINE

Development and Testing of the OPLS-AA/M Force Field for RNA.

Authors: Robertson MJ Qian Y Robinson MC et al.

Source: Journal of chemical theory and computation [J Chem Theory Comput] 2019 Apr 09; Vol. 15 (4), pp. 2734-2742. Date of Electronic Publication: 2019 Mar 12.

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