- Hao, M.-H., Haq, O., & Muegge, I. (2007). Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins. Journal of Chemical Information and Modeling, 47(6), 2242–2252. https://doi.org/10.1021/ci700189s
- Brameld, K. A., Kuhn, B., Reuter, D. C., Stahl, M., A. Brameld, K., Kuhn, B., C. Reuter, D., & Stahl, M. (2008). Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis. Journal of Chemical Information and Modeling, 48(1), 1–24. https://doi.org/10.1021/ci7002494
- Sitzmann, M., Weidlich, I. E., Filippov, I. v., Liao, C., Peach, M. L., Ihlenfeldt, W.-D., Karki, R. G., Borodina, Y. v., Cachau, R. E., & Nicklaus, M. C. (2012). PDB Ligand Conformational Energies Calculated Quantum-Mechanically. Journal of Chemical Information and Modeling, 52(3), 739–756. https://doi.org/10.1021/ci200595n
- Schärfer, C., Schulz-Gasch, T., Ehrlich, H. C., Guba, W., Rarey, M., & Stahl, M. (2013). Torsion angle preferences in druglike chemical space: A comprehensive guide. Journal of Medicinal Chemistry, 56(5), 2016–2028. https://doi.org/10.1021/jm3016816
- Liu, K., Watanabe, E., & Kokubo, H. (2017). Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. Journal of Computer-Aided Molecular Design, 31(2), 201–211. https://doi.org/10.1007/s10822-016-0005-2
- Sellers, B. D., James, N. C., Gobbi, A., D. Sellers, B., C. James, N., & Gobbi, A. (2017). A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments. Journal of Chemical Information and Modeling, 57(6), 1265–1275. https://doi.org/10.1021/acs.jcim.6b00614
- Peach, Megan L et al. “Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.” Journal of molecular recognition : JMR vol. 30,8 (2017): 10.1002/jmr.2618. doi:10.1002/jmr.2618
- Cavasin, A. T., Hillisch, A., Uellendahl, F., Schneckener, S., & Go, A. H. (2018). Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water. Journal of Chemical Information and Modeling, 58(5), 1005–1020. https://doi.org/10.1021/acs.jcim.8b00151
- Rai, B. K., Sresht, V., Yang, Q., Unwalla, R., Tu, M., Mathiowetz, A. M., & Bakken, G. A. (2019). Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations. Journal of Chemical Information and Modeling, 59(10), 4195–4208. https://doi.org/10.1021/acs.jcim.9b00373
- Winkler, D. A. (2020). Ligand entropy is hard but should not be ignored. Journal of Chemical Information and Modeling, 60(10), 4421–4423. https://doi.org/10.1021/acs.jcim.0c01146
- Fusani, L., Palmer, D. S., Somers, D. O., & Wall, I. D. (2020). Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. Journal of Chemical Information and Modeling, 60(3), 1528–1539. https://doi.org/10.1021/acs.jcim.9b00843
- John W. Liebeschuetz. The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein–Ligand X-ray Structures. Journal of Medicinal Chemistry 2021, 64 (11) , 7533-7543. https://doi.org/10.1021/acs.jmedchem.1c00228
- Nicolas Foloppe, I-Jen Chen. The reorganization energy of compounds upon binding to proteins, from dynamic and solvated bound and unbound states. Bioorganic & Medicinal Chemistry 2021, 51 , 116464. https://doi.org/10.1016/j.bmc.2021.116464
- Tong, J., & Zhao, S. (2021). Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation. Journal of Chemical Information and Modeling, 61(3), 1180–1192. https://doi.org/10.1021/acs.jcim.0c01197
- Gu, S., Smith, M. S., Yang, Y., Irwin, J. J., & Shoichet, B. K. (2021). Ligand Strain Energy in Large Library Docking. Journal of Chemical Information and Modeling, 61(9), 4331–4341. https://doi.org/10.1021/acs.jcim.1c00368
- Toenjes, S. T., Heydari, B. S., Albright, S. T., Hazin, R., Ortiz, M. A., Piedrafita, F. J., & Gustafson, J. L. (2023). Controlling Ibrutinib’s Conformations about Its Heterobiaryl Axis to Increase BTK Selectivity. ACS Medicinal Chemistry Letters. https://doi.org/10.1021/acsmedchemlett.2c00523
- Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey. The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. Journal of Chemical Information and Modeling 2022, 62 (7) , 1644-1653. https://doi.org/10.1021/acs.jcim.2c00043
- Dakota L. Folmsbee, David R. Koes, Geoffrey R. Hutchison. Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. Journal of Chemical Information and Modeling 2023, 63 (23) , 7401-7411. https://doi.org/10.1021/acs.jcim.3c01278
- Hongtao Zhao, Jonas Brånalt, Matthew Perry, Christian Tyrchan. The Role of Allylic Strain for Conformational Control in Medicinal Chemistry. Journal of Medicinal Chemistry 2023, 66 (12) , 7730-7755. https://doi.org/10.1021/acs.jmedchem.3c00446
- Ajay N. Jain, Alexander C. Brueckner, Ann E. Cleves, Mikhail Reibarkh, Edward C. Sherer. A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles. Journal of Medicinal Chemistry 2023, 66 (3) , 1955-1971. https://doi.org/10.1021/acs.jmedchem.2c01744
- Toenjes, S.T. et al. (2023) “Controlling Ibrutinib’s Conformations about Its Heterobiaryl Axis to Increase BTK Selectivity,” ACS Medicinal Chemistry Letters, 14(3), pp. 305–311. Available at: https://doi.org/10.1021/acsmedchemlett.2c00523.
-
Notifications
You must be signed in to change notification settings - Fork 0
gkxiao/strain_energy
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
About
No description or website provided.
Topics
Resources
Stars
Watchers
Forks
Packages 0
No packages published