Comparative Analysis of Protein Structure Alignments

January 2007
BMC Structural Biology;2007, Vol. 7, p50
Academic Journal
No abstract available.


Related Articles

  • StructAlign, a program for alignment of structures of DNA-protein complexes. Popov, Ya.; Galitsyna, A.; Alexeevski, A.; Karyagina, A.; Spirin, S. // Biochemistry (00062979);Nov2015, Vol. 80 Issue 11, p1465 

    Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of...

  • Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. Sierk, Michael L.; Smoot, Michael E.; Bass, Ellen J.; Pearson, William R. // BMC Bioinformatics;2010, Vol. 11, p146 

    Background: While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments...

  • Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Tyagi, M.; Sharma, P.; Swamy, C. S.; Cadet, F.; Srinivasan, N.; de Brevern, A. G.; Offmann, B. // Nucleic Acids Research;Jul2006, Vol. 34 Issue 11, pw119 

    Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein...

  • AS2TS system for protein structure modeling and analysis. Zemla, A.; Zhou, C. Ecale; Slezak, T.; Kuczmarski, T.; Rama, D.; Torres, C.; Sawicka, D.; Barsky, D. // Nucleic Acids Research;Jul2005, Vol. 33 Issue suppl 2, pw111 

    We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the...

  • A comprehensive analysis of non-sequential alignments between all protein structures. Abyzov, Alexej; Ilyin, Valentin A. // BMC Structural Biology;2007, Vol. 7, p78 

    Background: The majority of relations between proteins can be represented as a conventional sequential alignment. Nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. It is interesting to...

  • Structure and function analysis of flexible alignment regions in proteins. Pirovano, Walter; Van der Reijden, Anneke; Feenstra, K. Anton; Heringa, Jaap // BMC Bioinformatics;2009 Supplement 13, Vol. 10, Special section p1 

    The article focuses on a study on the structural features and functional importance of flexible alignment regions in proteins. The role of structural alignment in defining gold standards for different bioinformatics applications is mentioned. According to the authors, the helices and coils...

  • Pair hidden Markov models on tree structures. Y. Sakakibara // Bioinformatics;Jan2009 Supplement, Vol. 19, p232 

    Motivation: Computationally identifying non-coding RNA regions on the genome has much scope for investigation and is essentially harder than gene-finding problems for protein-coding regions. Since comparative sequence analysis is effective for non-coding RNA detection, efficient computational...

  • Recent Progress in Measuring Structural Similarity Between Proteins. Carugo, Oliviero // Current Protein & Peptide Science;Jun2007, Vol. 8 Issue 3, p219 

    Surprisingly, after at least two decades of researches focused on the analysis of the similarity between protein three-dimensional structures, several new comparison methods were proposed during the last few years. These are briefly summarized and commented below. Some of the newly developed...

  • State of the art: refinement of multiple sequence alignments. Chakrabarti, Saikat; Lanczycki, Christopher J; Panchenko, Anna R; Przytycka, Teresa M; Thiessen, Paul A; Bryant, Stephen H // BMC Bioinformatics;2006, Vol. 7, p499 

    Background: Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing...

  • Integrated web service for improving alignment quality based on segments comparison. Plewczynski, Dariusz; Rychlewski, Leszek; Yuzhen Ye; Jaroszewski, Lukasz; Godzik, Adam // BMC Bioinformatics;2004, Vol. 5, p98 

    Background: Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and prediction of structure from only sequence information. Over many years the secondary structure elements were used as...


Read the Article


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

Try another library?
Sign out of this library

Other Topics