Potential knowledge-based

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Sippl, M.J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5 229-235, 1995. 

With this database in hand, a simple question is asked [29] How different is a knowledge-based potential derived from this lattice database compared to the actual energy function used to construct the database If statistical errors are negligible and the knowledge-based method is perfect, the answer is expected to be They are exactly the same. ... 

Grzybowski BA, Ishchenko AV, Shimada J, Shakhnovich El. From knowledge-based potentials to combinatorial lead design in silico. Acc Chem Res 2002 35 261-9. 

Sotriffer CA, Gohlke H, Klebe G. Docking into knowledge-based potential fields a comparative evaluation of DrugScore. J Med Chem 2002 45 1967-70. 

CombiSMoG Uses a Monte Carlo ligand growth algorithm and knowledge-based potentials to combine combinatorial and rational strategies for generating biased compound libraries (86)... 

ProSa uses two kinds of knowledge-based potentials, one to model pairwise interactions between protein atoms, and one for protein-solvent interactions. 

Knowledge-based Potentials for Interactions between Protein Atoms... 

Let a, b, c, d, k, r) be a set of discrete variables that describe a particular conformation of a protein (see Table 11.1 and Figure 11.2). Then the knowledge-based potential for pair interactions is... 

Knowledge-based Potentials for Protein-solvent Interactions... 

W.A. Koppensteiner and M.J. Sippl. Knowledge-based potentials-back to the roots. Biochemistry (Mosc), 63 241-252,1998. 

A. Babajide, I.L. Hofacker, M.J. Sippl, and P.F. Stadler. Neutral networks in protein space - a computational study based on knowledge-based potentials of mean force. Folding Design, 2 261-269,1997. 

A. Babajide, R. Farber, I.L. Hofacker, J. Inman, A.S. Lapedes, and P.F. Stadler. Exploring protein-sequence space using knowledge-based potentials. J. Theo. Biol, 212 35—46,2001. 

Jonikas, M. A., Radmer, R. J., et al. (2009). Coarse-grained modehng of large RNA molecules with knowledge-based potentials and structural filters. RNA 15(2), 189—199. 

Sunyaev, S. R., Eisenhaber, F., Argos, P Kuznetsov, E. N. Tumanyan, V. G. (1998). Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino add types Proteins 31,225-46. 

Yang CY, Wang RX, Wang SM. M-score a knowledge-based potential scoring function accounting for protein atom mobility. J. Med. Chem. 2006 49 5903-5911. 

---