These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
4. Comparison of molecular mechanics, semi-empirical quantum mechanical, and density functional theory methods for scoring protein-ligand interactions. Yilmazer ND; Korth M J Phys Chem B; 2013 Jul; 117(27):8075-84. PubMed ID: 23758433 [TBL] [Abstract][Full Text] [Related]
5. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Pecina A; Eyrilmez SM; Köprülüoğlu C; Miriyala VM; Lepšík M; Fanfrlík J; Řezáč J; Hobza P Chempluschem; 2020 Nov; 85(11):2362-2371. PubMed ID: 32609421 [TBL] [Abstract][Full Text] [Related]
6. How accurate is the description of ligand-protein interactions by a hybrid QM/MM approach? Kollar J; Frecer V J Mol Model; 2017 Dec; 24(1):11. PubMed ID: 29234892 [TBL] [Abstract][Full Text] [Related]
7. Error estimates for (semi-)empirical dispersion terms and large biomacromolecules. Korth M Org Biomol Chem; 2013 Oct; 11(38):6515-9. PubMed ID: 23963227 [TBL] [Abstract][Full Text] [Related]
8. Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods. Antony J; Grimme S; Liakos DG; Neese F J Phys Chem A; 2011 Oct; 115(41):11210-20. PubMed ID: 21842894 [TBL] [Abstract][Full Text] [Related]
9. Calculations on noncovalent interactions and databases of benchmark interaction energies. Hobza P Acc Chem Res; 2012 Apr; 45(4):663-72. PubMed ID: 22225511 [TBL] [Abstract][Full Text] [Related]
10. Empirically corrected DFT and semi-empirical methods for non-bonding interactions. Foster ME; Sohlberg K Phys Chem Chem Phys; 2010 Jan; 12(2):307-22. PubMed ID: 20023806 [TBL] [Abstract][Full Text] [Related]
12. Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques. Bryce RA; Hillier IH Curr Pharm Des; 2014; 20(20):3293-302. PubMed ID: 23947649 [TBL] [Abstract][Full Text] [Related]
13. Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. Eyrilmez SM; Köprülüoğlu C; Řezáč J; Hobza P Chemphyschem; 2019 Nov; 20(21):2759-2766. PubMed ID: 31460692 [TBL] [Abstract][Full Text] [Related]
14. Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations. Heimdal J; Ryde U Phys Chem Chem Phys; 2012 Sep; 14(36):12592-604. PubMed ID: 22797613 [TBL] [Abstract][Full Text] [Related]
15. Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. Genheden S; Ryde U; Söderhjelm P J Comput Chem; 2015 Oct; 36(28):2114-24. PubMed ID: 26280564 [TBL] [Abstract][Full Text] [Related]
16. OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. Tuttle T; Thiel W Phys Chem Chem Phys; 2008 Apr; 10(16):2159-66. PubMed ID: 18404221 [TBL] [Abstract][Full Text] [Related]
17. Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II. Bobovská A; Tvaroška I; Kóňa J J Mol Graph Model; 2016 May; 66():47-57. PubMed ID: 27035259 [TBL] [Abstract][Full Text] [Related]
18. The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design. Lepšík M; Řezáč J; Kolář M; Pecina A; Hobza P; Fanfrlík J Chempluschem; 2013 Sep; 78(9):921-931. PubMed ID: 31986741 [TBL] [Abstract][Full Text] [Related]