Unknown

Dataset Information

0

Protein topology from predicted residue contacts.

ABSTRACT: Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the predicted interactions has allowed the method to be successfully applied to proteins up to 200 residues in length which is larger than any structure previously predicted using sequence data alone.

SUBMITTER: Taylor WR 

PROVIDER: S-EPMC3324774 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Protein topology from predicted residue contacts.

Taylor William R WR   Jones David T DT   Sadowski Michael I MI  

Protein science : a publication of the Protein Society 20111221 2

Residue contacts predicted from correlated positions in a multiple sequence alignment are often sparse and uncertain. To some extent, these limitations in the data can be overcome by grouping the contacts by secondary structure elements and enumerating the possible packing arrangements of these elements in a combinatorial manner. Strong interactions appear frequently but inconsistent interactions are down-weighted and missing interactions up-weighted. The resulting improved consistency in the pr  ...[more]

Similar Datasets

Unknown ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts.
| S-EPMC8218204 | biostudies-literature
Unknown Protein Residue Contacts and Prediction Methods.
| S-EPMC4894841 | biostudies-literature
Unknown Predicting protein residue-residue contacts using deep networks and boosting.
| S-EPMC3509494 | biostudies-literature
Unknown Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.
| S-EPMC8425427 | biostudies-literature
Unknown Predicting protein residue-residue contacts using random forests and deep networks.
| S-EPMC6419322 | biostudies-literature
Unknown Characteristics of protein residue-residue contacts and their application in contact prediction.
| S-EPMC4221654 | biostudies-literature
Unknown CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.
| S-EPMC4201158 | biostudies-literature
Unknown Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.
| S-EPMC4937781 | biostudies-literature
Unknown Assessing Predicted Contacts for Building Protein Three-Dimensional Models.
| S-EPMC5512107 | biostudies-literature
Unknown Identification of direct residue contacts in protein-protein interaction by message passing.
| S-EPMC2629192 | biostudies-literature