ProteinNet: a standardized data set for machine learning of protein structure
M AlQuraishi - BMC bioinformatics, 2019 - Springer
Background Rapid progress in deep learning has spurred its application to bioinformatics
problems including protein structure prediction and design. In classic machine learning …
problems including protein structure prediction and design. In classic machine learning …
Gene3D: expanding the utility of domain assignments
Abstract Gene3D http://gene3d. biochem. ucl. ac. uk is a database of domain annotations of
Ensembl and UniProtKB protein sequences. Domains are predicted using a library of profile …
Ensembl and UniProtKB protein sequences. Domains are predicted using a library of profile …
SCOP: a structural classification of proteins database
L Lo Conte, B Ailey, TJP Hubbard… - Nucleic acids …, 2000 - academic.oup.com
Abstract The Structural Classification of Proteins (SCOP) database provides a detailed and
comprehensive description of the relationships of known protein structures. The …
comprehensive description of the relationships of known protein structures. The …
The TIGRFAMs database of protein families
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov
models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) …
models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) …
DNA binding by the plant-specific NAC transcription factors in crystal and solution: a firm link to WRKY and GCM transcription factors
DH Welner, S Lindemose, JG Grossmann… - Biochemical …, 2012 - portlandpress.com
NAC (NAM/ATAF/CUC) plant transcription factors regulate essential processes in
development, stress responses and nutrient distribution in important crop and model plants …
development, stress responses and nutrient distribution in important crop and model plants …
The protein structure initiative structural genomics knowledgebase
Abstract The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB,
http://kb. psi-structuralgenomics. org) has been created to turn the products of the PSI …
http://kb. psi-structuralgenomics. org) has been created to turn the products of the PSI …
Molecular cloning of Frizzled-10, a novel member of the Frizzled gene family
J Koike, A Takagi, T Miwa, M Hirai, M Terada… - Biochemical and …, 1999 - Elsevier
The Frizzled genes encode WNT receptors. Frizzled-10 (FZD10), a novel member of the
Frizzled gene family, has been cloned and characterized. Nucleotide sequence analysis …
Frizzled gene family, has been cloned and characterized. Nucleotide sequence analysis …
DOG 1.0: illustrator of protein domain structures
A good picture is worth a thousand words. Schematic diagram of protein domain structures
with functional motifs/sites in a concise and illustrative drawing is greatly helpful for a broad …
with functional motifs/sites in a concise and illustrative drawing is greatly helpful for a broad …
SISYPHUS—structural alignments for proteins with non-trivial relationships
With the increasing amount of structural data, the number of homologous protein structures
bearing topological irregularities is steadily growing. These include proteins with circular …
bearing topological irregularities is steadily growing. These include proteins with circular …
G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool
E Belmonte-Reche, JC Morales - NAR genomics and …, 2020 - academic.oup.com
Abstract We present G4-iM Grinder, a system for the localization, characterization and
selection of potential G4s, i-Motifs and higher order structures. A robust and highly …
selection of potential G4s, i-Motifs and higher order structures. A robust and highly …