TY - JOUR

T1 - Standard‐geometry chains fitted to X‐ray derived structures

T2 - Validation of the rigid‐geometry approximation. II. Systematic searches for short loops in proteins: Applications to bovine pancreatic ribonuclease A and human lysozyme

AU - Palmer, Kathleen A.

AU - Scheraga, Harold A.

PY - 1992/4

Y1 - 1992/4

N2 - A rigid‐geometry approach to protein conformational searches has been used to calculate stable structures for localized regions of the molecules bovine pancreatic ribonuclease A and human lysozyme. The search method is essentially an application of the local deformation algorithm of Gō and Scheraga [Macromolecules, 3, 178–187 (1970)]. A series of local chain deformations is produced in the polypeptide chain. The deformations are screened to eliminate structures having serious atomic overlaps or energetically unreasonable backbone dihedral angles. The remaining structures are refined by energy minimization and the rms deviations of the energy‐minimized structures, relative to the native structures, are calculated. The correlation between low rms deviation and low energy is reasonably good, indicating that this method should be useful in generating a small number of candidate structures for further energy refinement. Further applications to proteins with an unknown structure, such as homology‐based modeling applications, should now be amenable to this type of procedure.

AB - A rigid‐geometry approach to protein conformational searches has been used to calculate stable structures for localized regions of the molecules bovine pancreatic ribonuclease A and human lysozyme. The search method is essentially an application of the local deformation algorithm of Gō and Scheraga [Macromolecules, 3, 178–187 (1970)]. A series of local chain deformations is produced in the polypeptide chain. The deformations are screened to eliminate structures having serious atomic overlaps or energetically unreasonable backbone dihedral angles. The remaining structures are refined by energy minimization and the rms deviations of the energy‐minimized structures, relative to the native structures, are calculated. The correlation between low rms deviation and low energy is reasonably good, indicating that this method should be useful in generating a small number of candidate structures for further energy refinement. Further applications to proteins with an unknown structure, such as homology‐based modeling applications, should now be amenable to this type of procedure.

UR - http://www.scopus.com/inward/record.url?scp=84986532418&partnerID=8YFLogxK

U2 - 10.1002/jcc.540130307

DO - 10.1002/jcc.540130307

M3 - Article

AN - SCOPUS:84986532418

SN - 0192-8651

VL - 13

SP - 329

EP - 350

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

IS - 3

ER -