Protein-ligand interactions scoring

Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL. Assessing scoring functions for protein-ligand interactions. J Med Chem 2004 47 3032-47. 

As discussed in the introduction, scoring functions still pose problems (see also Chapter 14). Some of these problems arise from insufficient consideration of details of favorable and unfavorable protein-ligand interactions. 

Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions a simplified potential approach. J Med Chem 1999 42 791-804. 

Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000 295 337-56. 

A. N. Jain, Scoring noncovalent protein-ligand interactions A continuous differentiable... 

Leach, A.R., Shoichet, B.K. and PeishofF, C.E. (2006) Prediction of protein-ligand interactions. Docking and scoring successes and gaps, foumal of Medicinal Chemistry, 49, 5852-5855. 

PLCALC tool for calculating the protein-ligand interaction free energy (HT) scores... 

Ishchenko, A. V., Shakhnovich, E. I. (2002) SMall Molecule Growth 2001 (SMoG2001) an improved knowledge-based scoring function for protein-ligand interactions. J Med Chem 45, 2770-2780. 

In the next step, we focused on a possible correlation between the derived AutoDock scoring values and the YETI protein-ligand interaction energies and the observed biological data. In an attempt to correlate the scoring values and... 

Pham T, Jain AN (2006) Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem 49 5856-5868... 

Scoring Function to Predict Protein-Ligand Interactions. 

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