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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Nh3D: A Reference Dataset of Structures of Non-homologous Proteins Resource Report Resource Website |
Nh3D: A Reference Dataset of Structures of Non-homologous Proteins (RRID:SCR_008212) | Nh3D | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. | duplication, element, feature, fragment, align, alignment, analysis, b-factor, dissimilar, homologous, protein, protein structure databases, residue, sequence, statistical, structurally, structure, topology | has parent organization: University of Toronto; Ontario; Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21286 | SCR_008212 | 2026-02-14 02:06:07 | 0 | ||||||||
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H-Invitational Database: Protein-Protein Interaction Viewer Resource Report Resource Website |
H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) | data or information resource, database | The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. | evolutionary, expression, function, gene, genetic, 3-dimensional, alternative splicing, disease, domain, human, interaction, isoform, localization, metabolic, microsatellite, molecular, non-coding, pathway, polymorphism, protein, rna, snps, structure, sub-cellular, transcript | has parent organization: National Institute of Advanced Industrial Science and Technology | nif-0000-10401 | SCR_008054 | H0InvDB PPI View | 2026-02-14 02:06:33 | 0 | |||||||||
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Secondary Structure Matching Resource Report Resource Website 100+ mentions |
Secondary Structure Matching (RRID:SCR_008365) | data or information resource, database | Secondary Structure Matching (SSM) is an interactive service for comparing protein structures in 3D. SSM compares to other protein matching services, see results here. It is used as a structure search engine in PISA service (Protein Interfaces, Surfaces and Assemblies). It queries may be launched from any web site, see instructions here and it is based on the CCP4 Coordinate Library, found here. The service provides for: -pairwise comparison and 3D alignment of protein structures -multiple comparison and 3D alignment of protein structures -examination of a protein structure for similarity with the whole PDB or SCOP archives -best Ca-alignment of compared structures -download and visualization of best-superposed structures using Rasmol (Unix/Linux platforms), Rastop (MS Windows machines) and Jmol (platform-independent server-side java viewer) -linking the results to other services - PDBe Motif, OCA, SCOP, GeneCensus, FSSP, 3Dee, CATH, PDBSum, SWISS-PROT and ProtoMap. Sponsors: The project is funded by the Collaborative Computational Project Number 4 in Protein Crystallography of the Biotechnology and Biological Sciences Research Council | alignment 3d, compare, interactive, interface, matching, multiple, pairwise, protein, secondary, structure, visualization | has parent organization: European Molecular Biology Laboratory | nif-0000-25563 | SCR_008365 | SSM | 2026-02-14 02:06:13 | 165 | |||||||||
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Homologous Sequences in Ensembl Animal Genomes Resource Report Resource Website 1+ mentions |
Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) | HOMOLENS | data or information resource, database | Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations. | ensembl, evolution, gene, alignment, comparative, homologous, molecular, nucleotide, organism, phylogenetic, phylogeny, protein, sequence, specie, structure, taxon, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Claude Bernard University Lyon 1; Lyon; France |
biotools:homolens, nif-0000-25424 | https://bio.tools/homolens | SCR_008356 | 2026-02-14 02:06:42 | 3 | ||||||||
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DNAtraffic Resource Report Resource Website |
DNAtraffic (RRID:SCR_008886) | DNAtraffic | data or information resource, database | DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. | dna, cell cycle, genome, nomenclature, ontology, structure, function, protein, chromatin remodeling, dna repair, damage response pathway, pathway, damage, drug, annotation, disease, dna network process, dna damage, gene sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland |
Norwegian Financial Mechanism PNRF-143-AI-1/07; Polish Ministry of Science and Higher Education N N301 165835 |
PMID:22110027 | Free | biotools:dnatraffic, nlx_151312 | https://bio.tools/dnatraffic | SCR_008886 | DNAtraffic database | 2026-02-14 02:06:43 | 0 | ||||
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NetAge Database Resource Report Resource Website 1+ mentions |
NetAge Database (RRID:SCR_010224) | NetAge | data or information resource, database | Database that contains gene sets and microRNA-regulated protein-protein interaction networks for longevity, age-related diseases and aging-associated processes. | longevity, protein-protein interaction, mirna-regulated protein-protein interaction network, gene, protein, mirna, biogerontology | has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel | Age-related disease, Aging | PMID:20186480 | Acknowledgement requested, Public | nlx_156769 | SCR_010224 | 2026-02-14 02:06:44 | 6 | ||||||
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OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | data or information resource, database | A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. | protein |
is listed by: OMICtools is related to: GermOnline has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21113020 PMID:17545180 |
Creative Commons Attribution-ShareAlike License, 2.5 | OMICS_01690 | SCR_011978 | Orthologous MAtrix | 2026-02-14 02:06:15 | 10 | ||||||
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BUSM Mass Spectrometry Resource Resource Report Resource Website |
BUSM Mass Spectrometry Resource (RRID:SCR_000823) | Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins. | systems biology technology center, mass spectrometry, glycoconjugate, oligosaccharide, protein | has parent organization: Boston University School of Medicine; Massachusetts; USA | NCRR P41RR010888 | nlx_152679 | SCR_000823 | Mass Spectrometry Resource for Biology and Medicine, Boston University School of Medicine Mass Spectrometry Resource, Boston University Mass Spectrometry Resource for Biology and Medicine | 2026-02-14 02:07:42 | 0 | |||||||
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ALZPEDIA Resource Report Resource Website 1+ mentions |
ALZPEDIA (RRID:SCR_017548) | AlzPedia | data or information resource, database | Collection of brief summaries of various genes and proteins implicated in pathophysiology of Alzheimer’s disease and other neurodegenerative disorders. It will be expanded over time and updated periodically in order to reflect current state of knowledge. | Summary, gene, protein, pathophysiology, Alzheimer, neurodegenerative, disorder | is related to: Alzheimer's Research Forum | Free, Freely available | SCR_017548 | 2026-02-14 02:06:54 | 2 | |||||||||
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DBAli. A Database of Structure Alignments. Resource Report Resource Website |
DBAli. A Database of Structure Alignments. (RRID:SCR_013418) | data or information resource, database | DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. It is not currently being updated; however, updates should resume in the near future. All pairwise structural comparisons in DBAli have been obtained using the MAMMOTH program developed in the group of Prof. Angel R. Ortiz. All multiple structure alignments in DBAli have been obtained using the SALIGN command in MODELLER developed in the group of Prof. Andrej Sali. | protein, protein structure comparison | nif-0000-02725 | SCR_013418 | DBAli | 2026-02-14 02:06:43 | 0 | ||||||||||
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ExTopoDB Resource Report Resource Website 1+ mentions |
ExTopoDB (RRID:SCR_013143) | ExTopoDB | data or information resource, database | A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction). | transmembrane protein, protein structure, topological model, blast, transmembrane, protein, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20601677 | Public | nlx_151724 | SCR_013143 | 2026-02-14 02:06:48 | 2 | |||||||
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TCMGeneDIT Resource Report Resource Website 10+ mentions |
TCMGeneDIT (RRID:SCR_013396) | data or information resource, database | TCMGeneDIT is a database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature. Integrated protein-protein interaction and biological pathways information collected from public databases are also available. In addition, the transitive relationships among genes, TCMs and diseases could be inferred through the shared intermediates. Furthermore, TCMGeneDIT is useful in deducing possible synergistic or antagonistic contributions of the prescription components to the overall therapeutic effects. TCMGeneDIT is a unique database of various association information about TCMs. The database integrating TCMs with life sciences and biomedical studies would facilitate the modern clinical research and the understanding of therapeutic mechanisms of TCMs and gene regulations. | drug, gene, antagonistic, biomedical, clinical, disease, ingredient, interaction, life science, literature, medicine, pathway, prescription, protein, regulation, research, synergistic, therapeutic | has parent organization: National Taiwan University; Taipei; Taiwan | National Science Council Taiwan ; NTU Frontier and Innovative Research Projects NTUPFIR-96R0107 |
PMID:18854039 | nif-0000-32868 | SCR_013396 | 2026-02-14 02:06:43 | 12 | ||||||||
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Biological Interaction database for Protein-nucleic Acid Resource Report Resource Website |
Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) | BIPA | data or information resource, database |
A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces. There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids. |
amino acid, interaction, nucleic acid, protein | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-20819 | http://www-cryst.bioc.cam.ac.uk/bipa | SCR_013371 | Biological Interaction database for Protein-nucleic Acid | 2026-02-14 02:06:24 | 0 | |||||||
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doRiNA Resource Report Resource Website 10+ mentions |
doRiNA (RRID:SCR_013222) | doRiNA | data or information resource, database | In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. | binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding |
is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
MDC Systems Biology Network ; BMBF ; Senate of Berlin; Berlin; Germany ; DFG |
PMID:22086949 | nlx_151321 | SCR_013222 | 2026-02-14 02:06:49 | 15 | |||||||
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FlyTrap- GFP Protein Trap Database Resource Report Resource Website 10+ mentions |
FlyTrap- GFP Protein Trap Database (RRID:SCR_013354) | data or information resource, database | The FlyTrap database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. Expression is under the control of endogenous promoter and enhancer elements, allowing for visualization of normal expression patterns. Drosophila proteins tagged with Green Fluorescent Protein (GFP) were created by insertion into genes of an artificial exon encoding GFP flanked by splice acceptor (SA) and splice donor (SD) sequences so that expression of GFP relies on splicing into mature mRNAs and in-frame fusion. | gfp-tagged protein, protein, protein trapping screen | has parent organization: Yale University; Connecticut; USA | nif-0000-02849 | SCR_013354 | FlyTrap | 2026-02-14 02:06:18 | 26 | |||||||||
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Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-02-14 02:06:50 | 2 | ||||||
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RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-02-14 02:06:25 | 2 | ||||||
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Mass Spectral Library Resource Report Resource Website 10+ mentions |
Mass Spectral Library (RRID:SCR_014668) | data or information resource, database | A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. | library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant | is listed by: Metabolomics Workbench | Available with the NIST MS Search Program for Windows | SCR_014668 | 2026-02-14 02:06:28 | 18 | ||||||||||
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Viral Integrated Structural Evolution Dynamic Database Resource Report Resource Website 1+ mentions |
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) | VIStEDD | data or information resource, database | Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. | Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation | has parent organization: Michigan State University; Michigan; USA | COVID-19 | NIGMS R01 GM108618; NIEHS K01 ES025435 |
PMID:32511397 | Free, Freely available | SCR_018793 | Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database | 2026-02-14 02:06:33 | 3 | |||||
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EPSD Eukaryotic Phosphorylation Site Database Resource Report Resource Website 1+ mentions |
EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) | EPSD | data or information resource, database | Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies. | protein, phosphorylation, site, eukaryotes, phosphoproteomic, data | has parent organization: Huazhong University of Science and Technology; Wuhan; China | Special Project on Precision Medicine under the National Key R&D Program 2017YFC0906600; the Natural Science Foundation of China 31671360; the Fundamental Research Funds for the Central Universities 2017KFXKJC001 |
Free, Freely available | SCR_016514 | Eukaryotic Phosphorylation Site Database, EPSD | 2026-02-14 02:06:31 | 1 |
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