Protein multiple alignments: sequence-based versus structure-based programs
نویسندگان
چکیده
منابع مشابه
PROMALS3D: a tool for multiple protein sequence and structure alignments
Although multiple sequence alignments (MSAs) are essential for a wide range of applications from structure modeling to prediction of functional sites, construction of accurate MSAs for distantly related proteins remains a largely unsolved problem. The rapidly increasing database of spatial structures is a valuable source to improve alignment quality. We explore the use of 3D structural informat...
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Protein fold recognition (threading) involves the prediction of a protein’s three-dimensional shape based on its similarity to a protein whose structure is known. Fold predictions are low resolution; no effort is made to rotate the protein’s component amino acid side chains into their correct spatial orientations. Rather, the goal is to recognize the protein family member that most closely rese...
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Structure comparison is used to reveal the similarity between protein structures. Every method has its own strength and weakness and the assessment parameters need to be appropriate to the original question on performance of the method. Here, we have assessed three multiple structure-based sequence alignment programs and compared their results. The results suggest that superfamily members which...
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Multiple Sequence alignments are a critical step in phylogeny inference. There is a lack of an appropriate approach which is capable of 1) finding the best global alignment and 2) automating and reproducing manual editing. Progressive alignment is an effective method for multiple Sequence alignments. However, its application in practice has also long been largely hampered because the alignment ...
متن کاملRNA-RNA interaction prediction based on multiple sequence alignments
MOTIVATION Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, O(N(6)) time and O(N(4)) space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is of...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2019
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btz236