X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2F3.2.1%2Flatex%2Funresman.tex;fp=doc%2F3.2.1%2Flatex%2Funresman.tex;h=6ec0dc5c37945b7dc0b88f6a2db5a01f7e2ed1de;hp=caaa183508d7078043ac3879e5773993fa205940;hb=cac632b968ece398a6176960617c770d9afd3f71;hpb=f5379d3246c4bd95e946c4d35d4a1c13e329c4cb diff --git a/doc/3.2.1/latex/unresman.tex b/doc/3.2.1/latex/unresman.tex index caaa183..6ec0dc5 100644 --- a/doc/3.2.1/latex/unresman.tex +++ b/doc/3.2.1/latex/unresman.tex @@ -958,13 +958,13 @@ to generate random conformations: THETPARPDB thetaml.5parm\\ ROTPARPDB scgauss.parm -For CSA, the best force field is 4P. For MD, the 1L2Y\_1LE1 force field is best for +For CSA, the best force field is 4P. For MD, the E0LL2Y force field is best for ab initio prediction but provides medium resolution (5 A for 60-residue proteins) and overemphasizes $\beta$-structures and has to be run with secondary-structure-prediction information. For prediction of the structure of mostly $\alpha$-protein, and for running dynamics of large proteins, the best is the GAB force field. All these force fields were trained by using our procedure of hierarchical optimization \cite{oldziej_2004,oldziej_2004_02}. -The 4P and 1L2Y\_1LE1 force fields have considerable power independent of structural class. +The 4P and E0LL2Y force fields have considerable power independent of structural class. The ALPHA, BETA, and ALPHABETA force fields (for CSA) were used in the CASP4 exercises and the CASP5 force field was used in the CASP5 exercise with some success; ALPHA predicts reasonably the structure of $\alpha$-helical proteins and is still not obsolete,