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Genomics database
The Open Protein Structure Annotation Network (TOPSAN) is a wiki designed to collect, share and distribute information about protein three-dimensional
Open protein structure annotation network
Open_protein_structure_annotation_network
a database of annotated protein models calculated by homology modeling TOPSAN the Open Protein Structure Annotation Network — a wiki designed to collect
Protein_structure_database
PSI:Biology-Materials Repository Open Protein Structure Annotation Network (TOPSAN), a wiki for annotation of protein structures determined by the PSI PSI Assessment
Protein_Structure_Initiative
Type of website edited collaboratively
button or link on the page being viewed. This will open an interface for writing, formatting, and structuring page content. The interface may be a source editor
Wiki
Study of the structure of every protein in a genome
developed a wiki-based approach namely Open protein structure annotation network (TOPSAN) for annotating protein structures emerging from high-throughput structural
Structural_genomics
Description of the structure and function of a genome
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome
DNA_annotation
Database of human proteins
protein has been classified into one or more of 49 different organelles and subcellular structures. In addition, the resource includes an annotation of
Human_Protein_Atlas
Protein structure prediction challenge
Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide
CASP
Computational analysis of large, complex sets of biological data
design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide
Bioinformatics
J (January 2018). "SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis". Nucleic Acids
List_of_biological_databases
Software for understanding biological data
bioinformatics algorithms had to be programmed by hand; for problems such as protein structure prediction, this proved difficult. Machine learning techniques such
Machine learning in bioinformatics
Machine_learning_in_bioinformatics
Biological database
association with other annotation databases, such as ZFIN (The Zebrafish Information Network), the Havana Group and GenBank. Manual annotation is currently more
Vertebrate Genome Annotation Project
Vertebrate_Genome_Annotation_Project
Identification and study of genomic sequences
organisms Identification of molecular structure from sequence alone. Since the very first sequences of the insulin protein were characterized by Fred Sanger
Sequence_analysis
Field dedicated to organizing and structuring biomedical data
(October 2006). "A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank". PLOS Computational Biology
Biocuration
Biomolecule consisting of chains of amino acid residues
responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily
Protein
SMIM14, which stabilizes the tertiary (and sometimes quaternary) structures of proteins. There are at least ten polyadenylation sequences in the 3’ UTR
Small integral membrane protein 14
Small_integral_membrane_protein_14
Large-scale study of proteins
covers the exploration of proteomes from the overall level of protein composition, structure, and activity. While the scale and complexity of the proteome
Proteomics
Protein-coding gene in humans
19 open reading frame 18 (c19orf18) is a protein which in humans is encoded by the c19orf18 gene. The gene is exclusive to mammals and the protein is
C19orf18
Grouping of proteins
(superfamily and family) annotations for all completely sequenced organisms SCOP and CATH - Classifications of protein structures into superfamilies, families
Protein_superfamily
BOINC based volunteer computing project researching protein folding
volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the
Rosetta@home
manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS)
BioJava
Type of machine learning model
Atlas, a database of 772 million structures of metagenomic proteins predicted using ESMFold. An LLM can also design proteins unlike any seen in nature. Nucleic
Large_language_model
Biological database of proteins
Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino
Structural Classification of Proteins database
Structural_Classification_of_Proteins_database
Protein-coding gene in the species Homo sapiens
Transmembrane protein 222 is a protein that in humans is encoded by the TMEM222 gene. One notable feature of the protein encoded by this gene is the presence
Transmembrane_protein_222
Form of biological modelling
reaction catalyzed by a protein using that protein's amino acid sequence as an input, and to infer the structure of a metabolic network based on the predicted
Metabolic_network_modelling
Type of analysis in molecular biology
depends on annotations found in existing databases, such as gene set membership in pathways, pathway topology, presence of genes in the global network etc.
Pathway_analysis
Molecule that carries genetic information
chromatin proteins, such as histones, compact and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping
DNA
Branch of machine learning
backpropagation algorithm in 1986. (p. 112 ). A 1988 network became state of the art in protein structure prediction, an early application of deep learning
Deep_learning
Discipline in genetics
direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues
Genomics
Protein-coding gene in humans
and DMAC1, Chromosome 9 Open Reading Frame 123 and Transmembrane Protein C9orf123 and Distal membrane-arm assembly complex protein 1. TMEM261 is located
DMAC1
(July 2011). "BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences". Nucleic Acids Research. 39
List of protein subcellular localization prediction tools
List_of_protein_subcellular_localization_prediction_tools
NCBThe Biomolecular Object Network Databank is a bioinformatics databank containing information on small molecule structures and interactions. The databank
Biomolecular Object Network Databank
Biomolecular_Object_Network_Databank
Mammalian protein found in Homo sapiens
protein expression summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2020-04-29. "AceView: Gene:C7orf50, a comprehensive annotation
Cholesin
Computer software for bioinformatics
biologists to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others
UGENE
different aspects of bacterial and archaeal biodiversity (BacDive), protein structures (ProteinPlus) and to comprehensive enzyme information (BRENDA). de.NBI
German Network for Bioinformatics Infrastructure
German_Network_for_Bioinformatics_Infrastructure
Protein-coding gene in humans
12 open reading frame 60 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-04-30. "I-TASSER server for protein structure and
C12orf60
Process by which a gene can code for multiple proteins
new tools for genome annotation and alternative splicing analysis. For instance, isoform.io, a platform guided by protein structure predictions, has evaluated
Alternative_splicing
Protein-coding gene in the species Homo sapiens
Adipose-secreted signaling protein has other aliases, UPF0687 Protein C20orf27, Chromosome 20 Open Reading Frame 27, Hypothetical Protein LOC54976, C20orf27,
Adipose-secreted signaling protein
Adipose-secreted_signaling_protein
Martin G (2001-12-01). "Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome". Computers & Chemistry
List of gene prediction software
List_of_gene_prediction_software
Aneuploid cell Aneuploidy Angelman syndrome Angiosperm Animal model Annealing Annotation Antibody Anticipation Anticoding strand Anticodon Antigen Antimorph Antiparallel
Index_of_genetics_articles
(chromosome 20 open reading frame 202) is a protein that in humans is encoded by the C20orf202 gene. In humans, this gene encodes for a nuclear protein that is
C20orf202
2011-03-25. "GraphML (.graphml)". "GRIB (.grb, .grib)". "GTF2.2: A Gene Annotation Format". wustl.edu. Archived from the original on 2022-01-19. Retrieved
List of filename extensions (F–L)
List_of_filename_extensions_(F–L)
Process in computational biology
prediction software Phylogenetic footprinting Protein function prediction Protein structure prediction Protein–protein interaction prediction Pseudogene (database)
Gene_prediction
Database of protein domains structures
domain-based resource for comparative genomics, functional annotation and protein network analysis". Nucleic Acids Research. 40 (Database issue): D465-71
CATH_database
Human C4orf19 gene
comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2021-12-17. "Homo sapiens chromosome 4 open reading
PGCKA1
methods use different properties of protein sequences and structures to find, characterize and annotate protein tandem repeats. Fournier D, Palidwor
List of protein tandem repeat annotation software
List_of_protein_tandem_repeat_annotation_software
Protein-coding gene in humans
Uncharacterized protein C20orf96 is a protein that in humans is encoded by the gene C20orf96. This protein is predicted to be a nuclear protein. The function
C20orf96
Evaluation of bioinformatic predictors of protein function
Assessment of Function Annotation (CAFA) is an ongoing community-driven experiment designed to evaluate computational methods for protein function prediction
Critical Assessment of Function Annotation
Critical_Assessment_of_Function_Annotation
Protein-coding gene in humans
similarity 216 member A is a protein that in humans is encoded by the FAM216A also known as the C12orf24 (Chromosome 12, open reading frame 24) gene. This
FAM216A
Biological database
Users of The BioGRID can search for their protein, chemical or publication of interest and retrieve annotation, as well as curated data as reported, by
BioGRID
Protein-coding gene in the species Homo sapiens
Protein TASOR 2 is a protein that in humans is encoded by the TASOR2 gene. The gene is also known as FAM208B and "chromosome 10 open reading frame 18"
TASOR2
Process of analysing text to extract information from it
analysis to study word frequency distributions, pattern recognition, tagging/annotation, information extraction, data mining techniques including link and association
Text_mining
Systematized collection of data in bioinformatics
Chemical-phenotype associations The Universal Protein Resource (UniProt) is an inclusive resource for protein sequence and annotation data. It is a comprehensive, first-class
Gene_Disease_Database
Protein family
head-to-tail cyclic structure through a disulfide bond with Cys3. The SMART database at the EMBL, as of May 2018, lists 3345 protein domains with structural
Stichodactyla_toxin
Mammalian protein found in Homo sapiens
Cardiac-enriched FHL2-interacting protein (CEFIP) is a protein encoded by the gene C10orf71 on chromosome 10 open reading frame 71. It is primarily understood
CEFIP
Protein-coding gene in humans
protein structure and function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2016-05-08. "TMEM156 - Transmembrane protein 156 - human protein (Proteomics)"
TMEM156
Protein found in humans
Chromosome 5 Open Reading Frame 47, or C5ORF47, is a protein which, in humans, is encoded by the C5ORF47 gene. It also goes by the alias LOC133491. The
Chromosome 5 open reading frame 47
Chromosome_5_open_reading_frame_47
Branch of bioinformatics
elements, and protein-protein interactions. By visualizing sequence alignments in the context of functional annotations and gene networks, researchers
Biological_data_visualization
American computer scientist (1968–2023)
of open domain question answering, multi-document summarization, large language models and the application of NLP in Bioinformatics, Social Network Analysis
Dragomir_R._Radev
Protein found in humans
Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood. C1orf94 gene
C1orf94
C15orf39 is a protein that in humans is encoded by the Chromosome 15 open reading frame 15 (C15orf39) gene. C15orf39 is located on chromosome 15 (15q24
C15orf39
(PlaToLoCo) has been developed, for visualization and annotation of low complexity regions in proteins. PlaToLoCo integrates and collects the output of five
List of software to detect low complexity regions in proteins
List_of_software_to_detect_low_complexity_regions_in_proteins
Biological cell regulation mechanisms
post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network. Gene regulation is essential
Regulation_of_gene_expression
Genomic data analysis software
regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization
GeWorkbench
Sequence of DNA that determines traits in an organism
predictions of about 30,000 protein-coding genes however that estimate has fallen to about 19,000 with the ongoing GENCODE annotation project. The number of
Gene
Collection of open-source Python software tools for computational biology
through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring
Biopython
Protein coding
A proposed structure for the protein can be found in the images for proposed structures. The secondary structure for the FAM178B protein is predicted
FAM178B
Human gene
CH. [A Novel Solution NMR Structure of Protein yst0336 from Saccharomyces cerevisiae https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61478&Dopt=s]
PBDC1
Protein-coding gene in the species Homo sapiens
is 1,763 base pairs long, and a protein that is 205 amino acids long. C20orf196 is involved in the DNA repair network. Gupta et al. identified C20orf196
SHLD1
Protein-coding gene in the species Homo sapiens
as Small Integral Membrane Protein 19, encodes the SMIM19 protein. SMIM19 is a confirmed single-pass transmembrane protein passing from outside to inside
SMIM19
Topical guide to software
printing protocols List of protein-ligand docking software List of protein structure prediction software List of manual image annotation tools List of mobile
Outline_of_software
Protein-coding gene in the species Homo sapiens
C9orf25 protein: 6 predicted Serine phosphorylation sites 1 predicted Tyrosine phosphorylation site 1 predicted prenylation site The secondary structure of
FAM219A
Human gene
73 (LRRC73) is a protein-coding gene, which, in Homo sapiens, is encoded by the LRRC73 gene.. Aliases: C6orf154, Chromosome 6 Open Reading Frame 154
LRRC73
but other Claudin2 superfamily proteins plays important roles in paracellular transport by contributing to the structure of gap junctions. In S. scrofa
TMEM202
Protein found in humans
TSBP1 is a protein that in humans is encoded by the TSBP1 gene. TSBP1 was previously known as C6orf10. C6orf10 is an open reading frame on chromosome 6
TSBP1
Small non-coding ribonucleic acid molecule
needed] The double-stranded RNA (dsRNA) structure of the hairpins in a pri-miRNA is recognized by a nuclear protein known as DiGeorge Syndrome Critical Region
MicroRNA
Open source software analysis package
for sequence alignment, rapid database searching with sequence patterns, protein motif identification (including domain analysis), and much more. The AJAX
EMBOSS
Protein-coding gene in the species Homo sapiens
Chromosome 20 open reading frame 141 (c20orf141) is a protein encoded by the c20orf141 gene in Humans (Homo sapiens). Human c20orf141 is located on the
C20orf141
Type of artificial intelligence approach
applied in multiple domains: construction site planning, inferring 3-D protein structures from X-ray crystallography, intelligent tutoring systems, and real-time
Blackboard_system
Human gene
Chromosome 5 open reading frame 15 (C5orf15) is a protein which in humans is encoded by the C5orf15 gene. It can also be referred to as keratinocyte-associated
Chromosome 5 open reading frame 15
Chromosome_5_open_reading_frame_15
Bioinformatics method
and candidate gene prioritization based on functional annotations and protein interactions network. Developed and maintained by the Division of Biomedical
Gene_set_enrichment_analysis
Protein-coding gene in the species Homo sapiens
Chromosome 4 open reading frame 51 (C4orf51) is a protein which in humans is encoded by the C4orf51 gene. The C4orf51 gene is located at 4q31.21 on the
C4orf51
Biomedical text analysis to extract relevant information and knowledge
research in areas of bibliography mapping, annotation extraction, protein named entity recognition, and protein ontology development. Curated databases such
Biomedical_text_mining
Region of DNA encouraging transcription
promoter regions. ORegAnno – Open Regulatory Annotation Database Archived 2021-03-21 at the Wayback Machine Identifying a Protein Binding Sites on DNA molecule
Promoter_(genetics)
Human protein and gene
(2012-05-08). "COFACTOR: an accurate comparative algorithm for structure-based protein function annotation". Nucleic Acids Research. 40 (W1): W471–W477. doi:10
FAM89A
Conversion of a gene's sequence into a mature gene product or products
protein or a functional RNA molecule. This process involves multiple steps, including the transcription of the gene's sequence into RNA. For protein-coding
Gene_expression
Information without a formal data model
or even millions of documents, or far more than manual approaches to annotation may permit. Several of these approaches are based upon the concept of
Unstructured_data
Concept in natural language processing
PMID 21122125. Chicco, D; Masseroli, M (2015). "Software suite for gene and protein annotation prediction and similarity search". IEEE/ACM Transactions on Computational
Semantic_similarity
Series of chemical reactions resulting in a cell response
Biomolecular Interaction Network Database, DIP – Database of Interacting Proteins, GNPV – Genome Network Platform Viewer, HPRD = Human Protein Reference Database
Biochemical_cascade
Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation" (PDF). Bioinformatics. 23 (1): 127–8. doi:10.1093/bioinformatics/btl529
List of phylogenetic tree visualization software
List_of_phylogenetic_tree_visualization_software
Weinberg Z, Ruzzo WL (August 2004). "Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy". Bioinformatics
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Spanish biologist
Bioinformatics, Network Biology and Machine Learning approaches. His group has developed systems in the areas of protein structure prediction, protein interactions
Alfonso_Valencia
Swiss-Prot/UniProtKB, a curated protein sequence database providing a high level of annotation, and STRING, which provides protein interaction networks and enrichment
Swiss Institute of Bioinformatics
Swiss_Institute_of_Bioinformatics
are two alpha helices. This protein is also predicted as a DNA binding protein. The protein may assume a tertiary structure of a coiled coil. Orthologs
Centrosomal_protein_15
of mass spectrometry data viewers and format converters. List of protein structure prediction software Cox, Jürgen; Neuhauser, Nadin; Michalski, Annette;
List of mass spectrometry software
List_of_mass_spectrometry_software
Intelligence in machines
the ability to approximate, in hours rather than months, the 3D structure of a protein. In 2023, it was reported that AI-guided drug discovery helped find
Artificial_intelligence
Method for outsourcing computing tasks to humans
of Washington, in which players compete to manipulate proteins into more efficient structures. A 2010 paper in science journal Nature credited Foldit's
Human-based_computation_game
Protein structure
(January 2017). "RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures". Nucleic Acids Research. 45 (D1):
Toroid_repeat_proteins
Chromosome 3 open reading frame 52
Chromosome 3 open reading frame 5 (C3orf52), also known as TTMP or TPA-Induced Transmembrane Protein (accession: NP_078892), is an uncharacterized protein encoded
C3orf52
Segment of nucleic acid that affects the expression of associated genes
Regulation of gene expression Cis-acting element Gene regulatory network Open Regulatory Annotation Database Operon DNA binding site Promoter Trans-acting factor
Regulatory_sequence
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