Docking small-molecule

Given the multitude of approaches now used to dock small molecules and peptides to proteins, why should the protein-protein docking problem require its own approaches Could one make do with the software packages developed for these related problems Unfortunately, the answer is usually no. 

Jones, G., Willet, P. Docking small-molecules ligands into active sites. Curr. Opin. Biotechnol 1995, 6, 652-656. 

Tliis list illustrates some diffbent strategies used to dock small molecules into proteins. A question mark indicates the method could have the ability indicated, but that the reference either did not use the ability or did not say it was used. 

G. Jones and P. Willett, Curr. Opin. Biotechnoi., 6, 652 (1995). Docking Small-Molecule Ligands into Active Sites. 

Some aspects, such as the computer representation and manipulation of proteins and nucleic acids, could not be covered. Even the modeling of the interactions of small molecules with proteins, as dealt with in docking software or software for de novo design could not be included in the Textbook, although chapters in the Handbook do treat these subjects. 

Molecular Modeling, Small Molecule Docking, and Computational Analysis... 

Taylor RD, Jewsbury PJ, Essex JW. A review of protein-small molecule docking methods. J Comput-Aided Mol Des 2002 16 151-66. 

Ingo Muegge and Matthias Rarey, Small Molecule Docking and Scoring. 

A very small molecule is significantly simpler to align or to dock because of its limited conformational space. The molecule is either rigid or has a low number of conformations, which can be enumerated. This is not the case anymore for molecules with more than, say, five rotatable bonds. Here, the number oflow-energy conformations is typically too high to justify an enumeration. Since several algorithmic engines for... 

Muegge, I. and Rarey, M. Small molecule docking and scoring. In... 

Stahl, M. and Schulz-Gasch, T. Practical database screening with docking tools. In Small Molecule-Protein Interaction, Waldmann, H. and Koppitz, M. (Eds.). Springer-Verlag, Berlin and Heidelberg, 2003, 127-150. 

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