Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Modeling protein loops using a phi i + 1, psi i dimer database

S Sudarsanam1, R F DuBose, C J March

  • 1Department of Protein Chemistry, Immunex Corporation, Seattle, Washington 98101, USA.

Protein Science : a Publication of the Protein Society
|July 1, 1995
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Classification of ovary abnormality using the probabilistic neural network (PNN).

Technology and health care : official journal of the European Society for Engineering and Medicine·2014
Same author

Clinical and molecular characterization of a novel PLIN1 frameshift mutation identified in patients with familial partial lipodystrophy.

Diabetes·2014
Same author

Computation and interpretation of vibrational spectra on the structure of Losartan using ab initio and Density Functional methods.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy·2014
Same author

Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy·2014
Same author

Pneumodescemetopexy with perfluoroethane (C2F6) for the treatment of acute hydrops secondary to keratoconus.

Eye (London, England)·2014
Same author

Molecular geometry, conformational, vibrational spectroscopic, molecular orbital and Mulliken charge analysis of 2-acetoxybenzoic acid.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy·2014
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

An automated method models protein loop backbones using a database of dihedral angles from the Protein Data Bank (PDB). This approach efficiently identifies near-native conformations without loop-closure algorithms.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein loops are crucial for protein function but challenging to model due to their conformational flexibility.
  • Existing methods for protein loop modeling often require computationally intensive loop-closure algorithms.

Purpose of the Study:

  • To develop an automated method for modeling protein loop backbones.
  • To create a database of allowed dihedral angles (phi and psi) for all 400 possible amino acid dimers.
  • To efficiently filter near-native loop conformations without relying on loop-closure algorithms.

Main Methods:

  • Constructed a database of phi and psi angles from non-redundant Protein Data Bank (PDB) entries.
  • Generated loop conformations by randomly sampling allowed dihedral angle pairs for each dimer.

Related Experiment Videos

  • Simulated protein loops of varying lengths (5-11 amino acids) and evaluated stereochemical consistency.
  • Developed a filtering method utilizing topological constraints of homologous proteins.

    • Main Results:

    • 50-80% of generated models exhibited no backbone stereochemical strain.
    • Simulated loops, when extended with flanking residues, showed that only a few conformations align correctly with protein topology.
    • The dimeric database proved sufficient for modeling loops in homologous proteins.
    • The developed filtering method successfully identified near-native loop conformations.

    Conclusions:

    • The automated method provides an efficient way to model protein loop backbones.
    • The method eliminates the need for loop-closure algorithms, simplifying the modeling process.
    • This approach enables the use of topological or disulfide constraints for filtering near-native conformations.