Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

  title={Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features},
  author={Wolfgang Kabsch and Christian A. Sander},
For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen‐bonding patterns… 

A New Type of φ, ψ Representation of the Protein Tertiary Structure and the Analysis of the Amino Acid Preferences for Specific Locations at Type-II β-Turn by Using 8000 Possible Kinds of Amino Acid Residues

A new type of representation of the protein tertiary structure can be used as a stereotyped finger printing for 125 protein molecules for a precise comparison of the relationship of the primary, secondary, and tertiary structures of homologous proteins.

Theoretical Aspects of Secondary Structure

Defined as the local spatial arrangement of the backbone atoms of a polypeptide chain, the secondary structure of a protein is often categorized as alpha (a)-helices, beta (b)-sheets, and others.

Cooperative effects in hydrogen‐bonding of protein secondary structure elements: A systematic analysis of crystal data using Secbase

This observation suggests that cooperative effects mutually polarizing spatially well‐aligned hydrogen bonds are present either in α helices and parallel β sheets whereas such influences seem to be lacking in 310 helics and antiparallel β sheets.

Secondary structure assignment that accurately reflects physical and evolutionary characteristics

A more accurate method for assigning secondary structure based on main chain geometry is developed, which also allows a more comprehensive assignment of secondary structure.

BCL::Score—Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

A tailored knowledge-based energy function is introduced that evaluates arrangement of secondary structure elements only and significantly enriches for native-like models in three different databases of 10,000–12,000 protein models in 80–94% of the cases.

Protein fold recognition from secondary structure assignments

  • R. RussellR. CopleyG. Barton
  • Computer Science, Biology
    Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences
  • 1995
A method for finding protein folds consistent with secondary structure assignments and imposed experimental restraints is described, which finds a set of plausible topologies for a protein of unknown structure, which can be inspected visually or tested by experiment.

Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results

An algorithm that operates independently of a predefined structure template is developed that contains features that reproduce the major secondary structure classes as well as defining conformations previously described only as random or undefined conformations.

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

A comparative analysis of families of homologous globular proteins to characterize and quantify the structural constraints and to identify ‘key’ residues if one or more structures are known.

The extended left‐handed helix: A simple nucleic acid‐binding motif

The results emphasize the need to classify the left‐handed helix as a viable nucleic acid recognition and binding motif, similar to previously identified motifs such as the helix‐turn‐helix, zinc fingers, leucine zippers, and others.

The use of amino acid patterns of classified helices and strands in secondary structure prediction.

This method predicts not only position of a secondary structure in a protein sequence but also the orientation of the secondary structure with respect to the core of the protein tertiary structure.



The anatomy and taxonomy of protein structure.

Information content in the circular dichroism of proteins.

A method is presented for predicting the secondary structure of a protein from its circular dichroism (CD) spectrum. Eight types of secondary structures are considered: helix; parallel and