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826 results

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Page 1
Guiding Medicinal Chemistry with Fragment Molecular Orbital (FMO) Method.
Heifetz A, James T, Southey M, Bodkin MJ, Bromidge S. Heifetz A, et al. Methods Mol Biol. 2020;2114:37-48. doi: 10.1007/978-1-0716-0282-9_3. Methods Mol Biol. 2020. PMID: 32016885 Review.
However, even when a target of interest is structurally enabled, visual inspection and force field-based molecular mechanics calculations cannot always explain the full complexity of the molecular interactions that are critical in drug design. ...The fragment …
However, even when a target of interest is structurally enabled, visual inspection and force field-based molecular mechanics calculat …
Interaction Analysis by Fragment Molecular Orbital Method for Drug Discovery Research.
Kawashita N. Kawashita N. Chem Pharm Bull (Tokyo). 2024;72(9):787-793. doi: 10.1248/cpb.c24-00448. Chem Pharm Bull (Tokyo). 2024. PMID: 39218703 Free article. Review.
The use of computational methods in drug discovery research has increased substantially in recent years. Computational chemistry techniques, such as quantum chemical calculations and molecular dynamics simulations, continue to be widely used. In this review, we focu …
The use of computational methods in drug discovery research has increased substantially in recent years. Computational chemistry tech …
Analyzing Interactions with the Fragment Molecular Orbital Method.
Fedorov DG. Fedorov DG. Methods Mol Biol. 2020;2114:49-73. doi: 10.1007/978-1-0716-0282-9_4. Methods Mol Biol. 2020. PMID: 32016886 Review.
Basic concepts in the analysis of binding using the fragment molecular orbital method are discussed at length: polarization, desolvation, and interaction. ...
Basic concepts in the analysis of binding using the fragment molecular orbital method are discussed at length: p …
Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method.
Heifetz A, James T, Southey M, Morao I, Fedorov DG, Bodkin MJ, Townsend-Nicholson A. Heifetz A, et al. Methods Mol Biol. 2020;2114:163-175. doi: 10.1007/978-1-0716-0282-9_11. Methods Mol Biol. 2020. PMID: 32016893 Review.
However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurate tools to explore receptor-ligand interactions. Visual inspection and molecular mechanics approaches cannot explain the full complex …
However, the ability of X-ray crystallography to guide the drug discovery process for GPCR targets is limited by the availability of accurat …
Taking Water into Account with the Fragment Molecular Orbital Method.
Okiyama Y, Fukuzawa K, Komeiji Y, Tanaka S. Okiyama Y, et al. Methods Mol Biol. 2020;2114:105-122. doi: 10.1007/978-1-0716-0282-9_7. Methods Mol Biol. 2020. PMID: 32016889 Review.
This chapter describes the current status of development of the fragment molecular orbital (FMO) method for analyzing the electronic state and intermolecular interactions of biomolecular systems in solvent. The orbital energies and the inter- …
This chapter describes the current status of development of the fragment molecular orbital (FMO) method for anal …
Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method.
Heifetz A, Sladek V, Townsend-Nicholson A, Fedorov DG. Heifetz A, et al. Methods Mol Biol. 2020;2114:187-205. doi: 10.1007/978-1-0716-0282-9_13. Methods Mol Biol. 2020. PMID: 32016895 Review.
Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, sensors, and transporters. Protein-protein interactions (PPIs) are a key part of their function. ...Quantum mechanical approaches are often to …
Proteins are vital components of living systems, serving as building blocks, molecular machines, enzymes, receptors, ion channels, se …
Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method.
Heifetz A, Townsend-Nicholson A. Heifetz A, et al. Methods Mol Biol. 2020;2114:177-186. doi: 10.1007/978-1-0716-0282-9_12. Methods Mol Biol. 2020. PMID: 32016894 Review.
However, even with the crystal structure in hand, our ability to understand GPCR-arrestin binding is limited by the availability of accurate tools to explore receptor-arrestin interactions. We applied fragment molecular orbital (FMO) method to explore …
However, even with the crystal structure in hand, our ability to understand GPCR-arrestin binding is limited by the availability of accurate …
The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems.
Sattasathuchana T, Xu P, Bertoni C, Kim YL, Leang SS, Pham BQ, Gordon MS. Sattasathuchana T, et al. J Chem Theory Comput. 2024 Mar 26;20(6):2445-2461. doi: 10.1021/acs.jctc.3c01309. Epub 2024 Mar 7. J Chem Theory Comput. 2024. PMID: 38450638
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advanta …
The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very …
Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.
Heifetz A, Aldeghi M, Chudyk EI, Fedorov DG, Bodkin MJ, Biggin PC. Heifetz A, et al. Biochem Soc Trans. 2016 Apr 15;44(2):574-81. doi: 10.1042/BST20150250. Biochem Soc Trans. 2016. PMID: 27068972 Free PMC article. Review.
We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 re …
We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment …
Computer-Aided Drug Design Using the Fragment Molecular Orbital Method: Current Status and Future Applications for SBDD.
Takaya D. Takaya D. Chem Pharm Bull (Tokyo). 2024;72(9):781-786. doi: 10.1248/cpb.c23-00839. Chem Pharm Bull (Tokyo). 2024. PMID: 39218702 Free article. Review.
In structure-based drug design (SBDD), including inhibitor design and in silico screening of drug target molecules, concordance with wet experimental data is important to provide insights on unique perspectives derived from calculations. Fragment molecular orbita …
In structure-based drug design (SBDD), including inhibitor design and in silico screening of drug target molecules, concordance with wet exp …
826 results