Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins

Madej, Thomas; Panchenko, Anna R.; Chen, Jie; Bryant, Stephen H.
January 2007
BMC Structural Biology;2007, Vol. 7, p23
Academic Journal
Background: To discover remote evolutionary relationships and functional similarities between proteins, biologists rely on comparative sequence analysis, and when structures are available, on structural alignments and various measures of structural similarity. The measures/scores that have most commonly been used for this purpose include: alignment length, percent sequence identity, superposition RMSD and their different combinations. More recently, we have introduced the "Homologous core structure overlap score" (HCS) and the "Loop Hausdorff Measure" (LHM). Along with these we also consider the "gapped structural alignment score" (GSAS), which was introduced earlier by other researchers. Results: We analyze the performance of these and other conventional measures at the task of ranking structure neighbors by homology, and we show that the HCS, LHM, and GSAS scores display considerably improved performance over the conventional measures of sequence or structural similarity. Conclusion: The HCS, LHM, and GSAS scores are easily computable quantities that allow users of structure-neighbor databases to more easily identify interesting structural similarities between proteins.


Related Articles

  • Algorithms for optimal protein structure alignment. Poleksic, Aleksandar // Bioinformatics;Nov2009, Vol. 25 Issue 21, p2751 

    Motivation: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment...

  • Drug delivery coalesces. Dove, Alan // Nature Biotechnology;Mar2000, Vol. 18 Issue 3, p249 

    Reports that scientists in the U.S. have developed a protein delivery system that responds to exogenous treatment with a small molecule. Creation of chimeric proteins that contain the coding sequence for a conditional aggregation domain (CAD) fused to a proinsulin; Accumulation of CAD fusions...

  • The Complex Nature of Protein Interactions. Gwynne, Peter // Genomics & Proteomics;Apr2003, Vol. 3 Issue 3, p37 

    Discusses the use of in silico methods to predict protein-protein reactions. Use of computers and software to predict the interactions on the basis of amino acid sequence information; Advantages of computational methods over other approaches in monitoring protein-protein interactions;...

  • Comprehensive Comparative Assessment of In-Silico Predictors of Disordered Regions. Zhen-Ling Peng; Kurgan, Lukasz // Current Protein & Peptide Science;Feb2012, Vol. 13 Issue 1, p6 

    Intrinsic disorder is relatively common in proteins, plays important roles in numerous cellular activities, and its prevalence was implicated in various human diseases. However, annotations of the disorder lag behind the rapidly increasing number of known protein chains. The last decade observed...

  • Insights into the sequence parameters for halophilic adaptation. Nath, Abhigyan // Amino Acids;Mar2016, Vol. 48 Issue 3, p751 

    The sequence parameters for halophilic adaptation are still not fully understood. To understand the molecular basis of protein hypersaline adaptation, a detailed analysis is carried out, and investigated the likely association of protein sequence attributes to halophilic adaptation. A two-stage...

  • Making automated multiple alignments of very large numbers of protein sequences. Sievers, Fabian; Dineen, David; Wilm, Andreas; Higgins, Desmond G. // Bioinformatics;Apr2013, Vol. 29 Issue 8, p989 

    Motivation: Recent developments in sequence alignment software have made possible multiple sequence alignments (MSAs) of >100 000 sequences in reasonable times. At present, there are no systematic analyses concerning the scalability of the alignment quality as the number of aligned sequences is...

  • ANARCI: antigen receptor numbering and receptor classification. Dunbar, James; Deane, Charlotte M. // Bioinformatics;1/15/2016, Vol. 32 Issue 2, p298 

    Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate...

  • The relationship between protein sequences and their gene ontology functions. Zhong-Hui Duan; Hughes, Brent; Reichel, Lothar; Perez, Dianne M.; Ting Shi // BMC Bioinformatics;2006 Supplement 4, Vol. 7, pS11 

    Background: One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been developed for the functional assignment of uncharacterized proteins. The...

  • Computational Time, Resources, and Quality Comparison of Protein Structure Superposition Algorithms. Hing, Ratana; Oxley, Alan // International Proceedings of Chemical, Biological & Environmenta;2012, Vol. 48, p95 

    Molecular superposition in three-dimensional space is an important task involving the placement of one structure in the space of another by minimizing the root-mean-square distance deviation of atoms between the two. Superposition methods can be used to interpret and understand molecular data....


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics