ArticleNucleic acids research2002
GTOP: a database of protein structures predicted from genome sequences.
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
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- Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability.Nature communications · 2019Article
- Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding.Scientific reports · 2018Article
- VaProS: a database-integration approach for protein/genome information retrieval.Journal of structural and functional genomics · 2016Article
- Prediction of protein-destabilizing polymorphisms by manual curation with protein structure.PloS one · 2012Article
- Mutational robustness of gene regulatory networks.PloS one · 2012Article
- Differences in dinucleotide frequencies of thermophilic genes encoding water soluble and membrane proteins.Journal of Zhejiang University. Science. B · 2011Article
- A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in rice (Oryza sativa L.).PLoS genetics · 2011Article
- Synonymous codon usage influences the local protein structure observed.Nucleic acids research · 2010Article
- Sub-AQUA: real-value quality assessment of protein structure models.Protein engineering, design & selection : PEDS · 2010Article
- DDBJ launches a new archive database with analytical tools for next-generation sequence data.Nucleic acids research · 2010Article
- Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements.The Journal of biological chemistry · 2009Article
- Translationally optimal codons associate with structurally sensitive sites in proteins.Molecular biology and evolution · 2009Article
- Development of an accurate classification system of proteins into structured and unstructured regions that uncovers novel structural domains: its application to human transcription factors.BMC structural biology · 2009Article
- Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins.BMC genomics · 2009Article
- The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions.Nucleic acids research · 2009Article
- VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts.Nucleic acids research · 2009Article
- Contact density affects protein evolutionary rate from bacteria to animals.Journal of molecular evolution · 2008Article
- Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies.Journal of bacteriology · 2008Article
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8 authors.
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Abstract
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues as to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a 'color-bar' format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/~genome/gtop.html.
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