Dataset Information

CORA--topological fingerprints for protein structural families.

ABSTRACT: CORA is a suite of programs for multiply aligning and analyzing protein structural families to identify the consensus positions and capture their most conserved structural characteristics (e.g., residue accessibility, torsional angles, and global geometry as described by inter-residue vectors/contacts). Knowledge of these structurally conserved positions, which are mostly in the core of the fold and of their properties, significantly improves the identification and classification of newly-determined relatives. Information is encoded in a consensus three-dimensional (3D) template and relatives found by a sensitive alignment method, which employs a new scoring scheme based on conserved residue contacts. By encapsulating these critical "core" features, templates perform more reliably in recognizing distant structural relatives than searches with representative structures. Parameters for 3D-template generation and alignment were optimized for each structural class (mainly-alpha, mainly-beta, alpha-beta), using representative superfold families. For all families selected, the templates gave significant improvements in sensitivity and selectivity in recognizing distant structural relatives. Furthermore, since templates contain less than 70% of fold positions and compare fewer positions when aligning structures, scans are at least an order of magnitude faster than scans using selected structures. CORA was subsequently tested on eight other broad structural families from the CATH database. Diagnostics plots are generated automatically and provide qualitative assistance for classifying newly determined relatives. They are demonstrated here by application to the large globin-like fold family. CORA templates for both homologous superfamilies and fold families will be stored in CATH and used to improve the classification and analysis of newly determined structures.

SUBMITTER: Orengo CA

PROVIDER: S-EPMC2144314 | biostudies-other | 1999 Apr

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

CORA--topological fingerprints for protein structural families.

Orengo C A CA

Protein science : a publication of the Protein Society 19990401 4

CORA is a suite of programs for multiply aligning and analyzing protein structural families to identify the consensus positions and capture their most conserved structural characteristics (e.g., residue accessibility, torsional angles, and global geometry as described by inter-residue vectors/contacts). Knowledge of these structurally conserved positions, which are mostly in the core of the fold and of their properties, significantly improves the identification and classification of newly-determ ...[more]

PMID: 10211816

Similar Datasets

Project description:BackgroundFocal dystonias are severe and disabling movement disorders of a still unclear origin. The structural brain networks associated with focal dystonia have not been well characterized. Here, we investigated structural brain network fingerprints in patients with blepharospasm (BSP) compared with those with hemifacial spasm (HFS), and healthy controls (HC). The patients were also examined following treatment with botulinum neurotoxin (BoNT).MethodsThis study included matched groups of 13 BSP patients, 13 HFS patients, and 13 HC. We measured patients using structural-magnetic resonance imaging (MRI) at baseline and after one month BoNT treatment, at time points of maximal and minimal clinical symptom representation, and HC at baseline. Group regional cross-correlation matrices calculated based on grey matter volume were included in graph-based network analysis. We used these to quantify global network measures of segregation and integration, and also looked at local connectivity properties of different brain regions.ResultsThe networks in patients with BSP were more segregated than in patients with HFS and HC (p < 0.001). BSP patients had increased connectivity in frontal and temporal cortices, including sensorimotor cortex, and reduced connectivity in the cerebellum, relative to both HFS patients and HC (p < 0.05). Compared with HC, HFS patients showed increased connectivity in temporal and parietal cortices and a decreased connectivity in the frontal cortex (p < 0.05). In BSP patients, the connectivity of the frontal cortex diminished after BoNT treatment (p < 0.05). In contrast, HFS patients showed increased connectivity in the temporal cortex and reduced connectivity in cerebellum after BoNT treatment (p < 0.05).ConclusionsOur results show that BSP patients display alterations in both segregation and integration in the brain at the network level. The regional differences identified in the sensorimotor cortex and cerebellum of these patients may play a role in the pathophysiology of focal dystonia. Moreover, symptomatic reduction of hyperkinesia by BoNT treatment was associated with different brain network fingerprints in both BSP and HFS patients.

Project description:BackgroundThe prediction of sites and products of metabolism in xenobiotic compounds is key to the development of new chemical entities, where screening potential metabolites for toxicity or unwanted side-effects is of crucial importance. In this work 2D topological fingerprints are used to encode atomic sites and three probabilistic machine learning methods are applied: Parzen-Rosenblatt Window (PRW), Naive Bayesian (NB) and a novel approach called RASCAL (Random Attribute Subsampling Classification ALgorithm). These are implemented by randomly subsampling descriptor space to alleviate the problem often suffered by data mining methods of having to exactly match fingerprints, and in the case of PRW by measuring a distance between feature vectors rather than exact matching. The classifiers have been implemented in CUDA/C++ to exploit the parallel architecture of graphical processing units (GPUs) and is freely available in a public repository.ResultsIt is shown that for PRW a SoM (Site of Metabolism) is identified in the top two predictions for 85%, 91% and 88% of the CYP 3A4, 2D6 and 2C9 data sets respectively, with RASCAL giving similar performance of 83%, 91% and 88%, respectively. These results put PRW and RASCAL performance ahead of NB which gave a much lower classification performance of 51%, 73% and 74%, respectively.Conclusions2D topological fingerprints calculated to a bond depth of 4-6 contain sufficient information to allow the identification of SoMs using classifiers based on relatively small data sets. Thus, the machine learning methods outlined in this paper are conceptually simpler and more efficient than other methods tested and the use of simple topological descriptors derived from 2D structure give results competitive with other approaches using more expensive quantum chemical descriptors. The descriptor space subsampling approach and ensemble methodology allow the methods to be applied to molecules more distant from the training data where data mining would be more likely to fail due to the lack of common fingerprints. The RASCAL algorithm is shown to give equivalent classification performance to PRW but at lower computational expense allowing it to be applied more efficiently in the ensemble scheme.

Dataset Information

CORA--topological fingerprints for protein structural families.

Publications

CORA--topological fingerprints for protein structural families.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets