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Items: 4

1.

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK.

J Mol Biol. 2009 Dec 11;394(4):747-63. doi: 10.1016/j.jmb.2009.09.049. Epub 2009 Sep 24.

2.

Molecular mechanics methods for predicting protein-ligand binding.

Huang N, Kalyanaraman C, Bernacki K, Jacobson MP.

Phys Chem Chem Phys. 2006 Nov 28;8(44):5166-77. Epub 2006 Sep 1. Review.

PMID:
17203140
3.

Computations of standard binding free energies with molecular dynamics simulations.

Deng Y, Roux B.

J Phys Chem B. 2009 Feb 26;113(8):2234-46. doi: 10.1021/jp807701h. Review.

4.

Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.

Peach ML, Cachau RE, Nicklaus MC.

J Mol Recognit. 2017 Aug;30(8). doi: 10.1002/jmr.2618. Epub 2017 Feb 24. Review.

PMID:
28233410

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