Relations between protein sequence and structure and their significance

Rooman, Marianne; Rodríguez, J. G.; Wodak, Shoshana J.

doi:10.1016/s0022-2836(05)80195-0

Cited by 54 publications

(31 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Importance of these structures was highlighted in loop modelling. Rooman et al [304] have already emphasized on the importance of the recurrent local structure motifs over secondary structure classification and on the relationship between structure and amino acid sequence. A complementary work was performed by Fetrow and Berg who showed that the use of local protein structure can reveal different distributions of rotamers classes [305].…”

Section: Structural Buildings Blocks Fetrow and Co-workers' Obtainedmentioning

confidence: 99%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

View full text Add to dashboard Cite

Protein structures are classically described as composed of two regular states, the α-helices and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple definition of secondary structures hides numerous limitations. In fact, the rules for secondary structure assignment are complex. Thus, numerous assignment methods based on different criteria have emerged leading to heterogeneous and diverging results. In the same way, 3 states may over-simplify the description of protein structure; 50% of all residues, i.e., the coil, are not genuinely described even when it encompass precise local protein structures.Description of local protein structures have hence focused on the elaboration of complete sets of small prototypes or "structural alphabets", able to analyze local protein structures and to approximate every part of the protein backbone. They have also been used to predict the protein backbone conformation and in ab initio / de novo methods. In this paper, we review different approaches towards the description of local structures, mainly through their description in terms of secondary structures and in terms of structural alphabets. We provide some insights into their potential applications.

show abstract

Section: Structural Buildings Blocks Fetrow and Co-workers' Obtainedmentioning

confidence: 99%

Local Protein Structures

Offmann¹,

Tyagi²,

Brevern

2007

CBIO

View full text Add to dashboard Cite

show abstract

“…Several approaches have been developed for the prediction of local structures based on fragment libraries [150][151][152][153][154][155][156][157] library by clustering frequently observed short sequence patterns (I-sites) in protein structures. An efficient local structure prediction method was developed based on this library [150,163].…”

Section: Beyond Secondary Structuresmentioning

confidence: 99%

From local structure to a global framework: recognition of protein folds

Joseph

Brevern

2014

J. R. Soc. Interface.

View full text Add to dashboard Cite

Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition.

show abstract

“…They demonstrated that, while not enough associations are derived to predict a complete protein structure, a number of reliable and predictive motifs do exist. In a similar study, Rooman et al (1990b) replace the standard secondary-structure identifiers with elements produced by structure motif discovery (see next section). Rooman et al (1989) take a number of sequence motifs, reported in the literature as characterizing local secondary structure, and subject them to a rigorous validation against a database of 75 proteins.…”

Section: Sequence and Sequence-structure Motifsmentioning

confidence: 99%

“…These motifs are correlated with four standard secondary structures. The four discovered classes are used in the sequence-structure analysis (Rooman et al, 1990b) discussed in the previous section. In a second experiment, Rooman et al (1990a) cluster heptamers and only retain motifs which contain, on average, 50 members.…”

Section: Structure Motifsmentioning

confidence: 99%

“…Zhang et al (1993) also tabulate the relative frequency of each of the amino acids for the central residue in their six discovered structure motifs. Finally, Rooman et al (1990b) obtain a property sequence motif for discovered heptamer structures. These sequences, however, are only weakly specific and are not likely to be predictive of the associated structure.…”

Section: Structure-sequence Motifsmentioning

confidence: 99%

See 1 more Smart Citation

Machine discovery of protein motifs

Conklin¹

1995

Mach Learn

View full text Add to dashboard Cite

Abstract. The investigation of relations between protein tertiary structure and amino acid sequence is a topic of tremendous importance in molecular biology. The automated discovery of recurrent patterns of structure and sequence is an essential part of this investigation. These patterns, known as protein motifs, are abstractions of fragments drawn from proteins of known sequence and tertiary structure. This paper has two objectives. The first is to introduce and define protein motifs, and provide a survey of previous research on protein motif discovery. The second is to present and apply a novel approach to protein motif representation and discovery, which is based on a spatial description logic and the symbolic machine learning paradigm of structured concept formation. A large database of protein fragments is processed using this approach, and several interesting and significant protein motifs are discovered.

show abstract

Relations between protein sequence and structure and their significance

Cited by 54 publications

References 25 publications

Local Protein Structures

Local Protein Structures

From local structure to a global framework: recognition of protein folds

Machine discovery of protein motifs

Contact Info

Product

Resources

About