Literature DB >> 28150234

CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences.

Natalie L Dawson1, Ian Sillitoe2, Jonathan G Lees2, Su Datt Lam2,3, Christine A Orengo2.   

Abstract

This chapter describes the generation of the data in the CATH-Gene3D online resource and how it can be used to study protein domains and their evolutionary relationships. Methods will be presented for: comparing protein structures, recognizing homologs, predicting domain structures within protein sequences, and subclassifying superfamilies into functionally pure families, together with a guide on using the webpages.

Keywords:  Annotation; Classification; Database; Function prediction; Protein domain; Sequence; Structural model prediction; Structure

Mesh:

Substances:

Year:  2017        PMID: 28150234     DOI: 10.1007/978-1-4939-6783-4_4

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  7 in total

Review 1.  Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach.

Authors:  Rossana Zaru; Michele Magrane; Sandra Orchard
Journal:  FEBS J       Date:  2019-11-03       Impact factor: 5.542

2.  De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads.

Authors:  Honglin Luo; Guanghua Huang; Jianbin Li; Qiong Yang; Jiajie Zhu; Bin Zhang; Pengfei Feng; Yongde Zhang; Xueming Yang
Journal:  Genes Genomics       Date:  2022-10-16       Impact factor: 2.164

3.  CATH: expanding the horizons of structure-based functional annotations for genome sequences.

Authors:  Ian Sillitoe; Natalie Dawson; Tony E Lewis; Sayoni Das; Jonathan G Lees; Paul Ashford; Adeyelu Tolulope; Harry M Scholes; Ilya Senatorov; Andra Bujan; Fatima Ceballos Rodriguez-Conde; Benjamin Dowling; Janet Thornton; Christine A Orengo
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

4.  Biological impact of mutually exclusive exon switching.

Authors:  Su Datt Lam; M Madan Babu; Jonathan Lees; Christine A Orengo
Journal:  PLoS Comput Biol       Date:  2021-03-02       Impact factor: 4.475

5.  Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome.

Authors:  François Bonnardel; Stuart M Haslam; Anne Dell; Ten Feizi; Yan Liu; Virginia Tajadura-Ortega; Yukie Akune; Lynne Sykes; Phillip R Bennett; David A MacIntyre; Frédérique Lisacek; Anne Imberty
Journal:  NPJ Biofilms Microbiomes       Date:  2021-06-15       Impact factor: 7.290

6.  3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures.

Authors:  Ruben Sanchez-Garcia; Carlos Oscar Sanchez Sorzano; Jose Maria Carazo; Joan Segura
Journal:  Molecules       Date:  2017-12-15       Impact factor: 4.411

7.  GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms.

Authors:  Yi-Wei Liu; Tz-Wei Hsu; Che-Yu Chang; Wen-Hung Liao; Jia-Ming Chang
Journal:  BMC Bioinformatics       Date:  2020-11-18       Impact factor: 3.169

  7 in total

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