Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.
Journal - Journal of molecular biology (ENGLAND )
The biological role, biochemical function, and structure of uncharacterized protein sequences is often inferred from their similarity to known proteins. A constant goal is to increase the reliability, sensitivity, and accuracy of alignment techniques to enable the detection of increasingly distant relationships. Development, tuning, and testing of these methods benefit from appropriate benchmarks for the assessment of alignment accuracy.Here, we describe a benchmark protocol to estimate sequence-to-sequence and sequence-to-structure alignment accuracy. The protocol consists of structurally related pairs of proteins and procedures to evaluate alignment accuracy over the whole set. The set of protein pairs covers all the currently known fold types. The benchmark is challenging in the sense that it consists of proteins lacking clear sequence similarity.Correct target alignments are derived from the three-dimensional structures of these pairs by rigid body superposition. An evaluation engine computes the accuracy of alignments obtained from a particular algorithm in terms of alignment shifts with respect to the structure derived alignments. Using this benchmark we estimate that the best results can be obtained from a combination of amino acid residue substitution matrices and knowledge-based potentials.Copyright 2000 Academic Press.
|ISSN : ||0022-2836|
|Mesh Heading : ||Algorithms Computational Biology Models, Molecular Protein Structure, Secondary Proteins Reproducibility of Results Sensitivity and Specificity Sequence Alignment Sequence Homology, Amino Acid metabolism|
|Mesh Heading Relevant : ||Protein Folding methods chemistry methods|
The role of protein structure in genomics.
Journal - FEBS letters (NETHERLANDS )
The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular structure and biological function. These tasks have triggered additional initiatives like structural genomics. The intention is to determine as many protein structures as possible, in the most efficient way, and to exploit the solved structures for the assignment of biological function to hypothetical proteins. We discuss the impact of these developments on protein classification, gene function prediction, and protein structure prediction.
|ISSN : ||0014-5793|
|Mesh Heading : ||Databases, Factual Models, Molecular Protein Structure, Secondary Proteins|
|Mesh Heading Relevant : ||Genome Protein Conformation chemistry genetics|
Sustained performance of knowledge-based potentials in fold recognition.
Journal - Proteins (UNITED STATES )
We describe the results obtained using fold recognition techniques in our third participation in the CASP experiment. The approach relies on knowledge-based potentials for alignment production and fold identification. As indicated by the increase in alignment quality and fold identification reliability, the predictions improved from CASP1 to CASP3. In particular, we identified structural relationships in which no known evolutionary link exists. Our predictions are based on single sequences rather than multiple sequence alignments. Additionally, we voluntarily submitted only a single model for each target because, in our view, submission of a single model is the most stringent test. We describe the methods used, the strategy adopted in the predictions, and the prediction results and discuss future work.
|ISSN : ||0887-3585|
|Mesh Heading : ||Algorithms Amino Acid Sequence Bacterial Proteins Carbon-Oxygen Lyases DNA-Binding Proteins Databases, Factual Escherichia coli Models, Molecular Molecular Sequence Data Proteins Ribosomal Proteins Sequence Alignment chemistry chemistry chemistry chemistry chemistry|
|Mesh Heading Relevant : ||Escherichia coli Proteins Protein Folding chemistry|