Protein superfamilles and domain superfolds

  title={Protein superfamilles and domain superfolds},
  author={Christine A. Orengo and David T. Jones and Janet M. Thornton},
As the protein sequence and structure databases expand rapidly a better understanding of the relationships between proteins is required. A classification is considered that extends the sequence-based superfamilies to include proteins with similar function and three-dimensional structures but no sequence similarity. So far there are only nine protein folds known to recur in proteins having neither sequence nor functional similarity. These folds dominate the structure database, representing more… 

From protein structure to function.

Structural classification of proteins: new superfamilies.

  • A. Murzin
  • Biology
    Current opinion in structural biology
  • 1996

The Classification of Protein Domains.

This chapter discusses the approaches and methods that are frequently used in the classification of proteins, with a specific emphasis on the classified protein domains and shows how the use of domain family annotations to assign structural and functional information is enhancing the authors' understanding of genomes.

Structure comparison and protein structure classifications

This chapter reviews the most popular methods and how they are combined with sequence comparison to recognize protein homologs and approaches to automatic domain boundary assignment algorithms in parallel with the construction of protein structure classifications.

Structure, function and evolution of multidomain proteins.

PASS2: an automated database of protein alignments organised as structural superfamilies

BackgroundThe functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar

Protein folds, functions and evolution.

The evolution of proteins and their functions is reviewed from a structural perspective in the light of the current database, finding that the number of new topologies is still increasing, although 25 new structures are now determined for each new topology.



Identification and classification of protein fold families.

Analysis of sequence and structure conservation within the larger families shows the globins to be the most highly conserved family and the TIM barrels the most weakly conserved.

A new approach to protein fold recognition

A new approach to fold recognition, whereby sequences are fitted directly onto the backbone coordinates of known protein structures, using a given sequence as a guide for the matching of sequences to backbone coordinates.

A data bank merging related protein structures and sequences.

Wedding the primary and tertiary structural data resulted in an 8-fold increase of data bank sequence entries over those associated with the known three-dimensional architectures alone.

A database of protein structure families with common folding motifs

The database makes explicitly visible architectural similarities in the known part of the universe of protein folds and may be useful for understanding protein folding and for extracting structural modules for protein design.

Structural relationships of homologous proteins as a fundamental principle in homology modeling

The main goal of the present work is to provide tools for the assessment of accuracy of modeling at a given level of sequence homology, and it is shown that both the topological differences of the protein backbones and the relative positions of corresponding side chains diverge with decreasing sequence identity.

Families and the structural relatedness among globular proteins

  • D. YeeK. Dill
  • Biology
    Protein science : a publication of the Protein Society
  • 1993
It is found that protein families are not tightly knit entities, by using an analogy to distributions of Euclidean distances.

Comparison of conformational characteristics in structurally similar protein pairs

This study presents further quantitative evidence that structure is remarkably well conserved in detail, as well as at the topological level, even when the sequences do not show similarity that is significant statistically.

Database of homology‐derived protein structures and the structural meaning of sequence alignment

A database of homology‐derived secondary structure of proteins (HSSP) is produced by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve, effectively increasing the number of known protein structures by a factor of five to more than 1800.

Protein structure alignment.