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Publication : journal of computer-aided molecular design

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Academic Journal

Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models

Authors : Reyna-Luna, Julieta¹ (AUTHOR); Soriano-Agueda, Luis² (AUTHOR); Vera, Christiaan Jardinez³ (AUTHOR)

Subjects: *CHEMICAL models; *THERMODYNAMIC cycles; *QUANTUM chemistry

Source: Journal of Computer-Aided Molecular Design. Jul2023, Vol. 37 Issue 7, p279-299. 21p.

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Academic Journal

Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies.

Authors : Mecklenfeld, Andreas^1,2 (AUTHOR); Raabe, Gabriele¹ (AUTHOR)

Subjects: *THERMODYNAMIC cycles; *SOLVATION; *CONDENSED matter

Source: Journal of Computer-Aided Molecular Design. Jan2020, Vol. 34 Issue 1, p71-82. 12p.

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Academic Journal

Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling.

Authors : Ma, Huaiqin¹ (AUTHOR); Shi, Qingwen¹ (AUTHOR); Li, Xuhua² (AUTHOR)

Subjects: *MOLECULAR dynamics; *COLLAGEN; *TISSUE engineering

Source: Journal of Computer-Aided Molecular Design. Jan2023, Vol. 37 Issue 1, p39-51. 13p.

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Academic Journal

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4.

Authors : Zou, Junjie^1,2 (AUTHOR); Tian, Chuan^1,2 (AUTHOR); Simmerling, Carlos^1,2 (AUTHOR)

Subjects: *PROTEIN-ligand interactions; *DRUG design; *BINDING energy

Source: Journal of Computer-Aided Molecular Design. Dec2019, Vol. 33 Issue 12, p1021-1029. 9p.

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Academic Journal

An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.

Authors : Olson, Brian^1,2 (AUTHOR); Cruz, Anthony^3,4 (AUTHOR); Chen, Lieyang^1,3 (AUTHOR)

Subjects: *SARS-CoV-2; *COVID-19; *SMALL molecules

Source: Journal of Computer-Aided Molecular Design. Dec2020, Vol. 34 Issue 12, p1219-1228. 10p.

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Academic Journal

Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding.

Authors : Samanta, Sudipta ; Mukherjee, Sanchita¹

Subjects: *CONFORMATIONAL analysis; *THERMODYNAMICS; *DNA damage

Source: Journal of Computer-Aided Molecular Design. Oct2017, Vol. 31 Issue 10, p891-903. 13p.

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Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4

Authors : Carlos Simmerling; Junjie Zou; Chuan Tian

Subjects: Protein Conformation; Thermodynamic integration; Crystallography, X-Ray

Source: J Comput Aided Mol Des

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Academic Journal

Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

Authors : Wu, Kuan-Wei¹; Chen, Po-Chin¹; Wang, Jun¹

Subjects: *GIBBS' free energy; *PROTEIN kinases; *THERMODYNAMICS

Source: Journal of Computer-Aided Molecular Design. Oct2012, Vol. 26 Issue 10, p1159-1169. 11p. 4 Diagrams, 4 Charts, 4 Graphs.

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Academic Journal

Thermodynamic integration to predict host-guest binding affinities.

Authors : Lawrenz, Morgan¹ ; Wereszczynski, Jeff¹; Ortiz-Sánchez, Juan¹

Subjects: *THERMODYNAMICS; *HOST-guest chemistry; *BINDING energy

Source: Journal of Computer-Aided Molecular Design. May2012, Vol. 26 Issue 5, p569-576. 8p. 2 Diagrams, 4 Charts, 2 Graphs.

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Academic Journal

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Authors : Hu, Yuan¹ ; Sherborne, Brad¹; Lee, Tai-Sung²

Subjects: *PROTON transfer reactions; *DRUG development; *THERMODYNAMIC cycles

Source: Journal of Computer-Aided Molecular Design. Jul2016, Vol. 30 Issue 7, p533-539. 7p.

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فلترة النتائج

Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models

Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies.

Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling.

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4.

An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.

Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding.

Blinded prediction of protein–ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4

Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.

Thermodynamic integration to predict host-guest binding affinities.

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

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