Parser for protein folding units

  title={Parser for protein folding units},
  author={Liisa Holm and Chris Sander},
  journal={Proteins: Structure},
General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X‐ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and… 

A thermodynamic definition of protein domains

This work presents a rigorous, thermodynamically-based approach that redefines structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures.

Identification of domains in protein structures from the analysis of intramolecular interactions.

A new computational approach is proposed that is based on the concept of domain as a compact and independent folding unit and on the analysis of the residue-residue energy interactions obtainable through classical all-atom force field calculations, and may complement the results given by other classification techniques.

Dictionary of recurrent domains in protein structures

A method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and recurrence is presented, which yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone.

A rapid test for identification of autonomous folding units in proteins.

It is shown that RAFT is able to predict whether a protein fragment will be structured if isolated from its parent domain, and is fast enough to mine the entire PDB for AFUs and provide a library of potential small stable folds.

Identification of structural domains in proteins by a graph heuristic

A novel automatic procedure for identifying domains from protein atomic coordinates, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non‐contiguous chain segments.

A bioinformatic web server to cut protein structures in terms of Protein Units.

Protein Peeling is a tool to better understand and analyze the organization of protein structures, and a dedicated bioinformatic web server is developed, given the 3D coordinates of a protein, which proposes an automatic identification of protein units (PUs).

Computational Methods for Domain Partitioning of Protein Structures

This chapter focuses on computational methods for domain partitioning with an analysis of basic premises about structural domains, reviews currently available methods, takes a detailed look into some partitioning algorithms, and discusses challenges and potential new approaches for the next generation of domain partitioned algorithms.

Automatic domain decomposition of proteins by a Gaussian Network Model

It is shown how the Gaussian Network Model (GNM), commonly used for determining motion, can be adapted to automatically classify domains in proteins, and similarities between this physical network model and graph theory implementation are apparent.

The hierarchical organization of molecular structure computations

This paper shows that the three methods that combine natural hierarchies with empirical hierarchies create decompositions which increase the efficiency of computations by as much as 50-fold and suggests that a speedup of about five can be expected just by virtue of having a decomposition.



Folding units in globular proteins.

  • A. LeskG. Rose
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1981
It turns out that there is more than one way to assemble the protein by self-association of its compact units, and the number of possible pathways is small--small enough to be exhaustively explored by a computer program.

Hierarchic organization of domains in globular proteins.

  • G. Rose
  • Biology
    Journal of molecular biology
  • 1979

Location of structural domains in proteins

Domains defined from interface area scans fit very well with globular structural regions identified by inspection of protein models, but do not in general correspond to the repeated structural units observed in some proteins by superposition studies.

The tree structural organization of proteins.

Identification of regions of potential flexibility in protein structures: Folding units and correlations with intron positions

It is suggested that the iterative estimation of flexible hinges may define an array of possible folding/unfolding paths, and that the exon–intron arrangement in the gene may be closely correlated with the folding process of the protein.

Compact units in proteins.

An explicit measure of geometric compactness called the coefficient of compactness is introduced and is applied to lysozyme and ribonuclease to discover their constituent compact units.

Location of domains in globular proteins

The globular fragments found in globins correlate with the two structural domains proposed previously4,19, and do not correlation with the three coding sequences separated by introns in the haemoglobin genes20–22.

Protein structure comparison by alignment of distance matrices.

A novel algorithm (DALI) for optimal pairwise alignment of protein structures that identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions is developed.

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

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 is developed.