| DYNAMICAL SIMULATED ANNEALING, ENERGY MINIMIZATION |
THE PROTEIN PART OF THE STRUCTURE WAS GENERATED IN A SIMULATED ANNEALING CALCULATION AND DOCKED WITH THE NUCLEOTIDE (IDEALIZED CONFORMATION) IN SUCCESSIVE ENERGY MINIMIZATIONS APPLYING FIRST INTRA, THEN INTERMOLECULAR NOE RESTRAINTS. THE CONFORMATION OF THE SINGLE STRANDED NUCLEOTIDE GETS DEFINED BY THE CONTACTS TO THE PROTEIN. FIFTY STRUCTURES OF THE COMPLEX WERE GENERATED BY SIMULATED ANNEALING AND ENERGY MINIMIZATION (MAXIMUM GRADIENT O.O2 KCAL/MOL/A2) THE NUCLEOTIDE CONFORMATION WAS KEPT FIXED DURING SIMULATED ANNEALING IN THE CONFORMATION OBTAINED IN THE FIRST STEP. TWENTY STRUCTURES WERE SELECTED WITH RESPECT TO RESTRAINT VIOLATIONS AND TOTAL ENERGY. |
1 |
