Document 0078
 DOCN  M9590078
 TI    Ranking potential binding peptides to MHC molecules by a computational
       threading approach.
 DT    9509
 AU    Altuvia Y; Schueler O; Margalit H; Department of Molecular Genetics,
       Hebrew University-Hadassah; Medical School, Jerusalem, Israel.
 SO    J Mol Biol. 1995 Jun 2;249(2):244-50. Unique Identifier : AIDSLINE
       MED/95302481
 AB    In this paper, an approach developed to address the inverse protein
       folding problem is applied to prediction of potential binding peptides
       to a specific major histocompatibility complex (MHC) molecule.
       Overlapping peptides, spanning the entire protein sequence, are threaded
       through the backbone coordinates of a known peptide fold in the MHC
       groove, and their interaction energies are evaluated using statistical
       pairwise contact potentials. With currently available tables for
       pairwise potentials, promising results are obtained for MHC-peptide
       complexes where hydrophobic interactions predominate. By ranking the
       peptides in an ascending order according to their energy values, it is
       demonstrated that, in most cases, known antigenic peptides are highly
       ranked. Furthermore, predicted hierarchies are consistent with
       experimental binding results. Currently, predictions of potential
       binding peptides to a specific MHC molecule are based on the
       identification of allele-specific binding motifs. However, it has been
       demonstrated that these motifs are neither sufficient nor strictly
       required to ensure binding. The computational procedure presented here
       succeeds in determining the MHC binding potential of peptides along a
       protein amino acid sequence, without relying on binding motifs. The
       proposed scheme may significantly reduce the number of peptides to be
       tested, identify good binders that do not necessarily show the known
       allele-specific binding motifs, and identify the best candidates among
       those with the motifs. In general, when structural information about a
       protein-peptide complex is available, the current application of the
       threading approach can be used to screen a large library of peptides for
       selection of the best binders to the target protein.
 DE    Amino Acid Sequence  Binding Sites  Comparative Study  Crystallography,
       X-Ray  Gene Products, tax/CHEMISTRY  HIV Envelope Protein
       gp120/CHEMISTRY  HIV-1  HLA-A2 Antigen/*CHEMISTRY  Molecular Sequence
       Data  Orthomyxovirus Type A, Human  Orthomyxoviruses Type B  Peptide
       Fragments/*CHEMISTRY  Reverse Transcriptase/CHEMISTRY
       Structure-Activity Relationship  Support, Non-U.S. Gov't  Support, U.S.
       Gov't, Non-P.H.S.  Viral Proteins/CHEMISTRY  JOURNAL ARTICLE

       SOURCE: National Library of Medicine.  NOTICE: This material may be
       protected by Copyright Law (Title 17, U.S.Code).