Docking proteins

One great advantage of the molecular mechanics model is that it can be applied to large molecules on your average PC. Apart from single molecular structure 

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Fukui Y, Hashimoto O, Sanui T, et al. Hematopoietic cell-specific CDM family protein DOCK-2 is essential for lymphocyte migration. Nature 2001 12 826-830. 

Structural properties of both AFA-PLN and WT-PLN bound to SER-CAla after reconstitution in a functional lipid bilayer environment were examined by 13C solid-state NMR.241 Chemical-shift assignments in all domains of AFA-PLN provide direct evidence for the presence of two terminal ot-helices connected by a linker region of reduced structural order that differs from previous findings on free PLN. A combination of the spectroscopic data with biophysical and biochemical data using flexible protein-protein docking simulations provides a structural basis for understanding the interaction between PLN and SERCala.244 Using a... 

In order to facilitate analysis of FeBABE produced fragments, the prey protein or biomolecule is labeled at one end with a tag that can be detected after electrophoresis, usually in a transfer blot. The tag can be a fusion tag, such as 6X His, or any other group that can be targeted with an antibody and detected. Alternatively, radiolabels and fluorescent labels have been used with prey molecules, including the use of end-labeled DNA to study where DNA binding proteins dock onto the oligonucleotide sequence. 

T. P. Lybrand, Ligand protein docking and rational drug design, Curr. Opin. Struct. Biol. 

CAChe 5.0, available in 2002, includes a new, more powerful, semiempirical method that uses the PM5 Hamiltonian, a MOPAC 2002 offering, modeling of molecules with up to 20,000 atoms, the inclusion of all main group elements in one semiempirical method, and using MOPAC AMl-d, supports the transition metals Pt, Fe, Cu, Ag, Mo, V, and Pd. Researchers can now import and display, in 3D, proteins from the Protein Data Bank (PDB), optimize proteins, dock ligands, and model reactions on protein molecules. 

Benyamini, H., Gunasekaran, K., Wolfson, H., and Nussinov, R. (2003). Beta2-micro-globulin amyloidosis Insights from conservation analysis and fibril modelling by protein docking techniques./. Mol. Biol. 330, 159-174. 

Lutz P. Ehrlich and Rebecca C. Wade, Protein-Protein Docking. 

Ritchie, W. and Kemp, G.J.L. Protein docking using spherical polar Fourier correlations. Proteins Struc., Func.,... 

Ritchie DW, Venkatraman V (2010) Ultrafast FFT protein docking on graphics processors. Bioinformatics 26 2398-2405... 

Figure 4.3 A prototype signal protein and its receptor is illustrated here. The human body relies on hundreds of different signal proteins docking into very specific and selective cell membrane receptor proteins to control which cell proteins are made or broken down and how the cell functions by sending specific chemical signals to other parts of the cell. The signal proteins may be produced by a nearby cell or reach its target from a distant cell through the blood stream.

Study Ligand-Protein Docking for information about drug design. Review movies showing interactions with a variety of ligand-protein systems. 

GOLD Automated ligand-protein docking program with genetic algorithm and force field-based scoring function... 

McConkey BJ, Sobolev V, Edelman M. The performance of current methods in ligand-protein docking. Curr Sci 2002 83 845-856. 

Xu M, Lill MA (2012) Utilizing experimental data for reducing ensemble size in flexible-protein docking. J Chem Inf Model 52(1) 187-198... 

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