Misleading local sequence alignments: implications for comparative protein modelling
نویسندگان
چکیده
منابع مشابه
Comparative Visualization of Protein Structure-Sequence Alignments
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...
متن کاملSequence Diversity Diagram for comparative analysis of multiple sequence alignments
BACKGROUND The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new vis...
متن کاملComparative modeling without implicit sequence alignments
MOTIVATION The number of known protein sequences is about thousand times larger than the number of experimentally solved 3D structures. For more than half of the protein sequences a close or distant structural analog could be identified. The key starting point in a classical comparative modeling is to generate the best possible sequence alignment with a template or templates. With decreasing se...
متن کاملLocal sequence alignments with monotonic gap penalties
MOTIVATION Sequence alignments obtained using affine gap penalties are not always biologically correct, because the insertion of long gaps is over-penalised. There is a need for an efficient algorithm which can find local alignments using non-linear gap penalties. RESULTS A dynamic programming algorithm is described which computes optimal local sequence alignments for arbitrary, monotonically...
متن کاملAlgorithms for Protein Comparative Modelling and Some Evolutionary Implications
Protein comparative modelling (CM) is a predictive technique to build an atomic model for a polypeptide chain, based on the experimentally determined structures of related pro teins (templates). It is widely used in Structural Biology, with applications ranging from mutation analysis, protein and drug design to function prediction and analysis, particu larly when there are no experimental str...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Protein Engineering Design and Selection
سال: 1998
ISSN: 1741-0126,1741-0134
DOI: 10.1093/protein/11.8.627