Scoring functions--the first 100 years.
The use of simple linear mathematical models to estimate chemical properties is not a new idea. Albert Einstein used very simple 'gravity-like' forces to explain the capillarity of different liquids in 1900-1901. Today such models are used in more complicated situations, and a great many have been developed to analyse interactions between proteins and their ligands. This is not surprising, since proteins are too complicated to model accurately without lengthy numerical analysis, and simple models often do at least as good a job in predicting binding constants as much more computationally expensive methods. One hundred years after Einstein's 'miraculous year' in which he transformed physics, it is instructive to recall some of his even earlier work. As approximations, 'scoring functions' are excellent, but it is dangerous to read too much into them. A few cautionary tales are presented for the beginner to the field of ligand affinity prediction by linear models.
Tame
Jeremy R H
JR
Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, 230-0045, Tsurumi, Yokohama, Japan. jtame@tsurumi.yokohama-cu.ac.jp
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D019295:Computational Biology; D015195:Drug Design; D019277:Entropy; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D011506:Proteins / Q000138:chemical synthesis / Q000378:metabolism; D013816:Thermodynamics
D008024:Ligands; D011506:Proteins