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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Kabat Database of Sequences of Proteins of Immunological Interest Resource Report Resource Website 1+ mentions |
Kabat Database of Sequences of Proteins of Immunological Interest (RRID:SCR_006465) | data or information resource, database | The Kabat Database determines the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. The Kabat Database searching and analysis tools package is an ASP.NET web-based portal containing lookup tools, sequence matching tools, alignment tools, length distribution tools, positional correlation tools and much more. The searching and analysis tools are custom made for the aligned data sets contained in both the SQL Server and ASCII text flat file formats. The searching and analysis tools may be run on a single PC workstation or in a distributed environment. The analysis tools are written in ASP.NET and C# and are available in Visual Studio .NET 2003/2005/2008 formats. The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time. Bence Jones proteins, mostly from human, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variability, was calculated for every position. Three peaks, at positions 24-34, 50-56 and 89-97, were identified and proposed to form the complementarity determining regions (CDR) of light chains. Subsequently, antibody heavy chain amino acid sequences were also aligned using a different numbering system, since the locations of their CDRs (31-35B, 50-65 and 95-102) are different from those of the light chains. CDRL1 starts right after the first invariant Cys 23 of light chains, while CDRH1 is eight amino acid residues away from the first invariant Cys 22 of heavy chains. During the past 30 years, the Kabat database has grown to include nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest. It has been used extensively by immunologists to derive useful structural and functional information from the primary sequences of these proteins. | functional, align, alignment, amino acid, antibody, antigen, biological, cdr, chain, class i, class ii, combining, complementarity, complex, delineation, heavy, histocompatibility, human, immunological, immunological database, light, macromolecule, mhc, molecule, nucleotide, position, protein, receptor, region, sequence, structural, t cell | has parent organization: Northwestern University; Illinois; USA | nif-0000-21233 | SCR_006465 | Kabat Database | 2026-09-12 01:01:42 | 2 | |||||||||
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SecStr Resource Report Resource Website 1+ mentions |
SecStr (RRID:SCR_006220) | SecStr | analysis service resource, data analysis service, production service resource, service resource | A tool to Predict the Secondary Structure of a protein from its amino acid sequence alone. The SecStr package uses six different secondary structure prediction methods (Nagano, Garnier et al., Burges et al., Chou and Fasman , Lim and Dufton and Hider). The results of those methods are combined into a Joint Prediction Histogram (JPH) as described by Hamodrakas, 1988 and Hamodrakas et al., 1982. As previously mentioned, the SecStr package contains computer programs making use of the secondary structure prediction methods of Nagano, Garnier et al., Burges et al., Chou and Fasman, Lim and Dufton and Hider. These programs were written in Fortran. The results of individual prediction methods are combined as described by Hamodrakas (1988), using a Perl program, to produce joint prediction histograms (JPH), for three types of secondary structure, which may be presented separately on a Java Applet. The output may be given either in text or graphics mode. For the latter a Java capable browser is required. | secondary structure, prediction, protein, algorithm, text, graphics |
is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
All rights are reserved for the whole or part of the program. Permission to use, Copy, And modify this software and its documentation is granted for academic use provided that:1. this copyright notice appears in all copies of the software and related documentation; 2. bugs will be reported to the authors. | nlx_151767 | SCR_006220 | SecStr - Secondary Structure Prediction, Secondary Structure Prediction, Secondary Structure Prediction of Proteins | 2026-09-12 01:01:41 | 7 | |||||||
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CW-PRED Resource Report Resource Website 10+ mentions |
CW-PRED (RRID:SCR_006188) | CW-PRED | analysis service resource, data analysis service, production service resource, service resource | A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif. | hidden markov model, gram-positive bacteria, protein, classification, cell-wall protein | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | Free for academic use, Acknowledgement requested | nlx_151733 | SCR_006188 | CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria | 2026-09-12 01:01:41 | 16 | |||||||
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orienTM Resource Report Resource Website |
orienTM (RRID:SCR_006218) | orienTM | analysis service resource, data analysis service, production service resource, service resource | A computer software that utilizes an initial definition of transmembrane segments to predict the topology of transmembrane proteins from their sequence. It uses position-specific statistical information for amino acid residues which belong to putative non-transmembrane segments derived from a statistical analysis of non-transmembrane regions of membrane proteins stored in the SwissProt database. Its accuracy compares well with that of other popular existing methods. | topology, prediction, transmembrane, protein, segment, algorithm, transmembrane protein |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
European Union ERBFMRXCT960019 | PMID:11477216 | nlx_151764 | SCR_006218 | orienTM - Orientation of TransMembrane proteins | 2026-09-12 01:01:41 | 0 | ||||||
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MCMBB Resource Report Resource Website 1+ mentions |
MCMBB (RRID:SCR_006198) | MCMBB | analysis service resource, data analysis service, production service resource, service resource | A web tool used in the discrimination of beta-barrel outer membrane proteins with a Markov chain model. MCMBB is a fast algorithm, which discriminates beta-barrel outer membrane proteins from globular proteins and from alpha-helical membrane proteins. The algorithm is based on a 1st order Markov Chain model, which captures the alternating pattern of hydrophilic-hydrophobic residues occurring in the membrane-spanning beta-strands of beta-barrel outer membrane proteins. The model achieves high accuracy in discriminating outer membrane proteins, since it can discriminate beta-barrel outer membrane with a correct classification rate of 90.08% and the globular proteins with a correct classification rate of 92.67%. When submitting alpha-helical membrane proteins, the method shows an accuracy of 100%. A score greater than zero, indicates that the protein is more likely to be a beta-barrel outer membrane protein, whereas a result lower than zero, indicates that the protein is probable not a beta-barrel. You may enter up to 1000 sequences in Fasta format. | algorithm, beta-barrel outer membrane protein, globular protein, alpha-helical membrane protein, markov chain model, beta-barrel, protein, outer membrane protein, classification, fasta, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
Acknowledgement requested | nlx_151742 | SCR_006198 | MCMBB: Markov Chain Model for Beta Barrels | 2026-09-12 01:01:41 | 2 | |||||||
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waveTM Resource Report Resource Website 1+ mentions |
waveTM (RRID:SCR_006199) | waveTM | analysis service resource, data analysis service, production service resource, service resource | A web tool for the prediction of transmembrane segments in alpha-helical membrane proteins. A sliding window of 20 residues is used in order to calculate an average residue hydrophobicity profile, using a hydrophobicity scale. Discrete Wavelet Transform is applied on the average residue hydrophobicity signal and the different frequency coefficients produced are adaptively thresholded so that a denoised signal is reconstructed. A dynamic programming algorithm processes the denoised signal to provide the optimal model for the number, the length and the location of membrane-spanning segments. The end points of the predicted segments are extended to include flanking hydrophobic residues. Topology prediction can also be obtained in conjunction with OrienTM (Liakopoulos et al, 2001). Analysis of a non-redundant test set, provides a ~95% per segment accuracy and ~90% per residue accuracy. Now, you can: * Run waveTM on a sequence * Browse the results obtained with the algorithm * View additional material concerning the hydrophobicity scale | wavelet, predict, transmembrane segment, alpha-helical membrane protein, protein, protein sequence, discrete wavelet transform, sequence, hydrophobicity scale, hydrophobicity, transmembrane protein, topology, transmembrane |
is related to: orienTM is related to: PRED-TMR has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
University of Athens; Athens; Greece | PMID:15107018 | Freely available | nlx_151743 | SCR_006199 | waveTM: Wavelet-based transmembrane segment prediction | 2026-09-12 01:01:41 | 3 | |||||
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PRED-TMBB Resource Report Resource Website 50+ mentions |
PRED-TMBB (RRID:SCR_006190) | PRED-TMBB | analysis service resource, data analysis service, production service resource, service resource | A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops. | protein, hidden markov model, prediction, membrane protein, beta-barrel outer membrane protein, gram-negative bacteria, topology, outer membrane protein, beta-barrel protein, probability, transmembrane strand, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
Greek Ministry of National Education and Religious Affairs | PMID:15215419 PMID:15070403 |
Acknowledgement requested | biotools:pred-tmbb, nlx_151734 | https://bio.tools/pred-tmbb | SCR_006190 | PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins | 2026-09-12 01:01:41 | 58 | ||||
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HOMSTRAD - Homologous Structure Alignment Database Resource Report Resource Website 10+ mentions |
HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) | HOMSTRAD | data or information resource, database | A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually. | homologous structure, protein, protein family, protein structure, align, 3d structure, structure-based alignment |
is listed by: OMICtools has parent organization: National Institute of Biomedical Innovation; Osaka; Japan |
PMID:14681395 | nif-0000-02977, OMICS_00976 | http://www-cryst.bioc.cam.ac.uk/homstrad | SCR_006544 | HOMologous STRucture Alignment Database | 2026-09-12 01:01:43 | 24 | ||||||
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PRED-TMR2 Resource Report Resource Website 1+ mentions |
PRED-TMR2 (RRID:SCR_006205) | PRED-TMR2 | analysis service resource, data analysis service, production service resource, service resource | A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2. | prediction, transmembrane, protein, algorithm, neural network, classification, transmembrane protein, protein classification, membrane protein, protein structure |
is related to: DAM-Bio has parent organization: PRED-TMR |
European Union ERBFMRXCT960019 | PMID:10469822 | nlx_151766 | SCR_006205 | PRED-TMR2: Prediction of Transmembrane regions in proteins | 2026-09-12 01:01:41 | 1 | ||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | analysis service resource, data analysis service, production service resource, service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-09-12 01:01:42 | 3 | |||||
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PRED-TMR Resource Report Resource Website 1+ mentions |
PRED-TMR (RRID:SCR_006203) | PRED-TMR | analysis service resource, data analysis service, production service resource, service resource | A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). | predict, transmembrane segment, protein, algorithm, sequence, membrane protein, protein structure, transmembrane region, hydrophobicity analysis |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory is parent organization of: PRED-TMR2 |
European Union ERBFMRXCT960019 | PMID:10360978 | nlx_151765 | SCR_006203 | PRED-TMR: A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database | 2026-09-12 01:01:41 | 7 | ||||||
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Worldwide Protein Data Bank (wwPDB) Resource Report Resource Website 1000+ mentions |
Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) | wwPDB | data or information resource, database | Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations. | 3-dimentional, bioinformatics, protein, research, structure, macromolecule, structural data, 3d spatial image, gold standard |
is used by: Ligand Expo is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Proteopedia - Life in 3D is related to: NRG-CING is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: PDBj - Protein Data Bank Japan is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PDB Validation Server is related to: Structural Antibody Database is parent organization of: PDB-Dev works with: PDB-REDO |
BBSRC ; DOE ; European Molecular Biology Laboratory ; European Union ; Heidelberg; Germany ; Japan Science and Technology Agency ; NBDC - National Bioscience Database Center ; NCI ; NIDDK ; NIGMS ; NIH ; NINDS ; NLM ; NSF ; Wellcome Trust |
PMID:14634627 | Free, Freely available | nif-0000-23903, r3d100011104 | https://doi.org/10.17616/R3462V | SCR_006555 | World Wide Protein DataBank, wwPDB, Worldwide Protein Data Bank (wwPDB), World Wide Protein Data Bank, Worldwide Protein DataBank | 2026-09-12 01:01:43 | 1340 | ||||
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Protein Ligand Database Resource Report Resource Website |
Protein Ligand Database (RRID:SCR_006980) | PLD | data or information resource, database | It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design. | binding energy, biomolecular, interaction, ligand, protein, protein sequence | nif-0000-20902 | http://www-mitchell.ch.cam.ac.uk/pld/ | SCR_006980 | Protein Ligand Database | 2026-09-12 01:01:45 | 0 | ||||||||
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Dali database Resource Report Resource Website 1+ mentions |
Dali database (RRID:SCR_006974) | data or information resource, database | Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword. | protein, protein 3d structure, protein structure | has parent organization: University of Helsinki; Helsinki; Finland | PMID:20457744 | nif-0000-02719 | SCR_006974 | Dali Database | 2026-09-12 01:01:45 | 4 | ||||||||
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Consensus CDS Resource Report Resource Website 100+ mentions |
Consensus CDS (RRID:SCR_006729) | CCDS | data or information resource, database | Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly. | human genome sequence, human protein, mouse genome sequence, mouse protein, protein coding region, gene, genome sequence, genome, sequence, gene annotation, protein, gold standard |
is listed by: OMICtools is related to: Entrez Gene is related to: HomoloGene is related to: MapViewer is related to: VEGA has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: University of California at Santa Cruz; California; USA |
PMID:24217909 PMID:22434842 PMID:19498102 |
The community can contribute to this resource, Acknowledgement requested | nif-0000-02645, OMICS_01535 | http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi | SCR_006729 | CCDS Database, NCBI Consensus CDS protein set, NCBI CCDS Database | 2026-09-12 01:01:44 | 242 | |||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-09-12 01:01:44 | 524 | |||||
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HIV-1 Human Protein Interaction Database Resource Report Resource Website 10+ mentions |
HIV-1 Human Protein Interaction Database (RRID:SCR_006879) | HIV-1 Human Protein Interaction Database | data or information resource, database | A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication. | protein-protein interaction, protein, interaction, cellular protein |
is related to: VirHostNet: Virus-Host Network has parent organization: NCBI |
Human immunodeficiency virus, Type 1 | NIAID contract N01-AI-05415; NIAID N01-AI-70042 |
PMID:18927109 PMID:19025396 PMID:19262354 |
Acknowledgement requested | nif-0000-02964 | SCR_006879 | HIV-1: Human Protein Interaction Database, Human immunodeficiency virus type 1 human protein interaction database at NCBI | 2026-09-12 01:01:44 | 13 | ||||
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MyHits Resource Report Resource Website 10+ mentions |
MyHits (RRID:SCR_006757) | data or information resource, database | Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. | protein, domain, motif, sequence, predictor, markov, model, gene, expression, mysql, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:17545200 | Free | nif-0000-02962, biotools:myhits | https://bio.tools/myhits | SCR_006757 | MyHit | 2026-09-12 01:01:44 | 41 | ||||||
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Rice Kinase Database Resource Report Resource Website |
Rice Kinase Database (RRID:SCR_006990) | RKD | data or information resource, database | It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps. | chromosomal map, genomic data, genomic information, phylogenetic tree, protein, proteomic, rice kinase | nif-0000-20910 | SCR_006990 | Rice Kinase Database | 2026-09-12 01:01:45 | 0 | |||||||||
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CuticleDB Resource Report Resource Website 10+ mentions |
CuticleDB (RRID:SCR_007045) | cuticleDB | data or information resource, database | A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin. | genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitin, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
University of Athens; Athens; Greece ; NIAID AI055624 |
PMID:15453918 | biotools:cuticledb, nif-0000-02708 | https://bio.tools/cuticledb | SCR_007045 | CuticleDB - A relational database of Arthropod cuticular proteins | 2026-09-12 01:01:45 | 14 |
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