| Abstract: | A reduced representation of paroteins has been developed for use in restraint satisfaction calculations with dynamic simulated annealing. Each amino acid residue is represented by up to four spherical virtual atoms. The virtual bonds and excluded volume of these atoms has ben parameterized by analysis of 83 protein structures determined at high resolution by X-ray crystallography. The use of the new representation in NOE distance restraint satisfaction has been compared with the standard all-atom represntation for the determination of the structures of crambin, eshistatin, and protein G. Using the reduced representation, there is a 30-fold decrease in the computer time needed for generatin a single structure, and up to a 20-fold decrease in the time taken to produce an acceptable structure compared to using the all-atom representation. The root mean square deviation between the mean structure obtain with all-atom and reduced representation si between 1.5 and 1.7 Å for Cα atoms. The new representation is adequate for describing the “low-resolution” features of protein structure such as the general fold and the positions of the secondary structure for more detailed refinement with the full all-atom representation. © 1993 Wiley-Liss, Inc. |
