Protein folds and families: sequence and structure alignments
نویسندگان
چکیده
منابع مشابه
Protein folds and families: sequence and structure alignments
Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming meth...
متن کاملComparative 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...
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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...
متن کاملCombining sequence and structure information in protein alignments
For distantly related proteins, alignmentsbased on structural information are more reliable than traditional sequence alignments. However, when structural comparison leaves some ambiguity in alignment, sequence information can provide valuable additional information to discriminate between multiple alternatives. In this paper we present a Bayesianmodel that incorporates sequence information int...
متن کاملUse of residue pairs in protein sequence-sequence and sequence-structure alignments.
Two new sets of scoring matrices are introduced: H2 for the protein sequence comparison and T2 for the protein sequence-structure correlation. Each element of H2 or T2 measures the frequency with which a pair of amino acid types in one protein, k-residues apart in the sequence, is aligned with another pair of residues, of given amino acid types (for H2) or in given structural states (for T2), i...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 1999
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/27.1.244