156 related articles for article (PubMed ID: 33570387)
1. Efficient
Öhlknecht C; Katz S; Kröß C; Sprenger B; Engele P; Schneider R; Oostenbrink C
J Chem Inf Model; 2021 Mar; 61(3):1193-1203. PubMed ID: 33570387
[TBL] [Abstract][Full Text] [Related]
2. Saturation Mutagenesis by Efficient Free-Energy Calculation.
Jandova Z; Fast D; Setz M; Pechlaner M; Oostenbrink C
J Chem Theory Comput; 2018 Feb; 14(2):894-904. PubMed ID: 29262673
[TBL] [Abstract][Full Text] [Related]
3. Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.
Kasper P; Christen P; Gehring H
Proteins; 2000 Aug; 40(2):185-92. PubMed ID: 10842335
[TBL] [Abstract][Full Text] [Related]
4. Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates.
Weber IT; Harrison RW
Protein Sci; 1997 Nov; 6(11):2365-74. PubMed ID: 9385639
[TBL] [Abstract][Full Text] [Related]
5. Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors.
de Ruiter A; Oostenbrink C
J Chem Theory Comput; 2012 Oct; 8(10):3686-95. PubMed ID: 26593013
[TBL] [Abstract][Full Text] [Related]
6. Enhancing the promiscuity of a member of the Caspase protease family by rational design.
Öhlknecht C; Petrov D; Engele P; Kröß C; Sprenger B; Fischer A; Lingg N; Schneider R; Oostenbrink C
Proteins; 2020 Oct; 88(10):1303-1318. PubMed ID: 32432825
[TBL] [Abstract][Full Text] [Related]
7. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
Pitera JW; Kollman PA
Proteins; 2000 Nov; 41(3):385-97. PubMed ID: 11025549
[TBL] [Abstract][Full Text] [Related]
8. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
Sham YY; Chu ZT; Tao H; Warshel A
Proteins; 2000 Jun; 39(4):393-407. PubMed ID: 10813821
[TBL] [Abstract][Full Text] [Related]
9. Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.
Caldararu O; Olsson MA; Misini Ignjatović M; Wang M; Ryde U
J Comput Aided Mol Des; 2018 Oct; 32(10):1027-1046. PubMed ID: 30203229
[TBL] [Abstract][Full Text] [Related]
10. Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation.
Cummins PL; Gready JE
J Comput Chem; 2005 Apr; 26(6):561-8. PubMed ID: 15726569
[TBL] [Abstract][Full Text] [Related]
11. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions.
Froloff N; Windemuth A; Honig B
Protein Sci; 1997 Jun; 6(6):1293-301. PubMed ID: 9194189
[TBL] [Abstract][Full Text] [Related]
12. Analysis of the binding energies of testosterone, 5alpha-dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody.
Nordman N; Valjakka J; Peräkylä M
Proteins; 2003 Jan; 50(1):135-43. PubMed ID: 12471606
[TBL] [Abstract][Full Text] [Related]
13. Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability-Large-Scale Validation of MD-Based Relative Free Energy Calculations.
Steinbrecher T; Zhu C; Wang L; Abel R; Negron C; Pearlman D; Feyfant E; Duan J; Sherman W
J Mol Biol; 2017 Apr; 429(7):948-963. PubMed ID: 27964946
[TBL] [Abstract][Full Text] [Related]
14. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
Archontis G; Simonson T; Karplus M
J Mol Biol; 2001 Feb; 306(2):307-27. PubMed ID: 11237602
[TBL] [Abstract][Full Text] [Related]
15. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
Misini Ignjatović M; Caldararu O; Dong G; Muñoz-Gutierrez C; Adasme-Carreño F; Ryde U
J Comput Aided Mol Des; 2016 Sep; 30(9):707-730. PubMed ID: 27565797
[TBL] [Abstract][Full Text] [Related]
16. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.
Jiao D; Zhang J; Duke RE; Li G; Schnieders MJ; Ren P
J Comput Chem; 2009 Aug; 30(11):1701-11. PubMed ID: 19399779
[TBL] [Abstract][Full Text] [Related]
17. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches.
Raman EP; Lakkaraju SK; Denny RA; MacKerell AD
J Comput Chem; 2017 Jun; 38(15):1238-1251. PubMed ID: 27782307
[TBL] [Abstract][Full Text] [Related]
18. Predicting proteinase specificities from free energy calculations.
Mekonnen SM; Olufsen M; Smalås AO; Brandsdal BO
J Mol Graph Model; 2006 Oct; 25(2):176-85. PubMed ID: 16386933
[TBL] [Abstract][Full Text] [Related]
19. Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability.
Thakur A; Gizzio J; Levy RM
J Phys Chem B; 2024 Feb; 128(7):1656-1667. PubMed ID: 38350894
[TBL] [Abstract][Full Text] [Related]
20. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.
Kamerlin SC; Haranczyk M; Warshel A
J Phys Chem B; 2009 Feb; 113(5):1253-72. PubMed ID: 19055405
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
