CSA: comprehensive comparison of pairwise protein structure alignments
نویسندگان
چکیده
CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl.
منابع مشابه
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic
MOTIVATION The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate...
متن کاملVorolign - fast structural alignment using Voronoi contacts
UNLABELLED Vorolign, a fast and flexible structural alignment method for two or more protein structures is introduced. The method aligns protein structures using double dynamic programming and measures the similarity of two residues based on the evolutionary conservation of their corresponding Voronoi-contacts in the protein structure. This similarity function allows aligning protein structures...
متن کاملMultiple sequence alignment by conformational space annealing.
We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA databases, the 82 families from the BAliB...
متن کاملStructSorter: A Method for Continuously Updating a Comprehensive Protein Structure Alignment Database
Advances in protein crystallography and homology modeling techniques are producing vast amounts of high resolution protein structure data at ever increasing rates. As such, the ability to quickly and easily extract structural similarities is a key tool in discovering important functional relationships. We report on an approach for creating and maintaining a database of pairwise structure alignm...
متن کاملTOPOFIT-DB and T-Server: A Database of structural alignments and a server for one-to-all protein structure comparisons based on the TOPOFIT method
Studies on protein structural alignments address several questions: functional characterization and annotation of proteins, evolutionary relationship between species, identification of rigid and flexible parts, identification of invariant and variable regions, domain identification, protein engineering, modeling, molecular dynamics, etc. To accomplish a specific goal, one may need to perform on...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 40 شماره
صفحات -
تاریخ انتشار 2012