DEVELOPMENT AND APPLICATION OF A HIERARCHICAL PROTOCOL FOR AB INITIO PREDICTION

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. For the past several years, we have been developing a united residue force field UNRES. The UNRES force field has been derived as a potential of mean force of the united-residue chain and ultimately parameterized based on the concept of a hierarchical protein energy landscape. Protein structure prediction was demonstrated in extensive tests on known proteins and in four blind-prediction experiments CASP3, CASP4, CASP5, and CASP6 in years 1998, 2000, 2002, and 2004. Recently we implemented the UNRES force field in molecular dynamics. Initial results from UNRES molecular dynamics runs shows that we are able to simulate folding events which take place in a microsecond- or even a millisecond-time scale. Our research plan for the period APR/2006-MAR/2007 are: i) continuation of development of the molecular dynamics code for the UNRES force field; ii) continuation of the fine-tuning of the UNRES force field using a revised hierarchical potential-function optimization protocol; iii) enhancement of the capability of different global search methods for the UNRES force field; iv) participation in CASP7 exercise.