HYPER: A hierarchical algorithm for automatic determination of protein dihedral-angle constraints and stereospecific C(β)H2 resonance assignments from NMR data

Roberta Tejero, Daniel Monleon, Bernardo Celda, Robert Powers, Gaetano T. Montelione

Research output: Contribution to journalArticle

14 Scopus citations

Abstract

A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and C(β)H2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of φ, ψ, and (χ1) dihedral angles and C(β)H2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-coupling constraints. Dihedral-angle constraints are valuable for restricting conformational space and improving convergence in three- dimensional structure calculations. HYPER computes the set of φ, ψ, and (χ1) dihedral angles and C(β)H2 stereospecific assignments that are consistent with up to nine intraresidue and sequential distance bounds, two pairs of relative distance bounds, thirteen homo- and heteronuclear scalar coupling bounds, and two pairs of relative scalar coupling constant bounds. The program is designed to be very flexible, and provides for simple user modification of Karplus equations and standard polypeptide geometries, allowing it to accommodate recent and future improved calibrations of Karplus curves. The C code has been optimized to execute rapidly (0.3-1.5 CPU-sec residue-1 using a 5°grid) on Silicon Graphics R8000, R10000 and Intel Pentium CPUs, making it useful for interactive evaluation of inconsistent experimental constraints. The HYPER program has been tested for internal consistency and reliability using both simulated and real protein NMR data sets.

Original languageEnglish (US)
Pages (from-to)251-264
Number of pages14
JournalJournal of Biomolecular NMR
Volume15
Issue number3
DOIs
StatePublished - Dec 1 1999

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Keywords

  • Automated analysis of NMR data
  • Constraint propagation
  • Grid search
  • Protein NMR

ASJC Scopus subject areas

  • Biochemistry
  • Spectroscopy

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