...agreementBack to the TopThe networks are adapted from: A graphical view of the world of protein-protein interaction databases, by Tomas Klingström and Dariusz Plewczynski. ICM, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Poland. The work was supported by Polish Ministry of Science and Higher Education N301 159735 grant.The networks are visualized with Cytoscape Web.BIND - Biomolecular Interaction Network Database. Protein-Protein Interactions. Genetic Interaction NetworksDetailsFreePSI-MIBRITE - Functional Hierarchies and Binary Relationships of Biological Entities. Protein...

...protein 253111SCAMP310067Secretory carrier membrane protein 354111IL18BP10068Interleukin 18 binding protein55111RWDD2B10069C21orf6 protein56110CDH81006Cadherin 857110DPP310072Q53GT458111SNUPN10073Snurportin 159111HUWE110075Upstream regulatory element binding protein 160110PTPRU10076Protein tyrosine phosphatase61111TSSC410078Tumor suppressing subtransferable candidate 462111CDH91007Cadherin 963111PDCD710081Q6IEG364111USH1C10083Q7RTU865111PQBP110084Polyglutamine binding protein 166110EDIL310085Q8N61067111COL4A3BP10087B3KUB768111CDH101008Cadherin 1069111ARPC510092Actin related protein 2/3 complex subunit 570111ARPC410093C9JJ5971111ARPC310094ARP2/3 protein complex subunit p2172111ARPC1B10095A4D27573111ACTR310096P6115874111ACTR210097ARP2 actin-related protein 2 homolog75110TSPAN310099A6NEH476111CDH111009Cadherin 1177110ADA100Adenosine deaminase78110TSPAN110103Tetraspan 179110PPIF10105Peptidylprolyl isomerase F80110CTDSP210106CTD carboxy-terminal domain81111ARPC210109Q53R1982111CDH121010Cadherin 1283111SGK210110Serum/glucocorticoid regulated kinase 284111RAD5010111RAD5085111KIF20A10112Kinesin family member 20A86110PREB10113Q9HCU587111HIPK310114Homeodomain interacting protein kinase 388110FEM1B10116FEM1 beta89110ACTR1B10120Actin related protein 1B90111ACTR1A10121Actin related protein 1A91110ARL4C10123Q53R1092110ARL4A10124ADP ribosylation factor like 4A93110RASGRP110125B2RA8994111DNAL410126O9601595111ZNF26310127Zinc finger protein...

...August 2013We now have information about ~550 resources!. Visual navigation added May 2010Click the 'Database interactions' link on the left menu to access. Major updateAll resources were recently reviewed and many new ones were added Get the StatsDetailed Pathguide resource statistics now available Pathguide PublishedPlease cite the Pathguide PublicationProtein-Protein Interactions  Database Name (Order: alphabetically | by web popularity alphabetically | by web popularity ) Full RecordAvailabilityStandards2P2Idb - The...

...August 2013We now have information about ~550 resources!. Visual navigation added May 2010Click the 'Database interactions' link on the left menu to access. Major updateAll resources were recently reviewed and many new ones were added Get the StatsDetailed Pathguide resource statistics now available Pathguide PublishedPlease cite the Pathguide PublicationProtein-Protein Interactions  Database Name (Order: alphabetically | by web popularity alphabetically | by web popularity ) Full RecordAvailabilityStandards2P2Idb - The...

...Sp3 (SPR-2). 21. ENSG00000174840 - 201626 2'-phosphodiesterase 22. ENSG00000183087 GAS6 2621 Growth-arrest-specific protein 6 precursor (GAS-6). 23. ENSG00000196104 SPOCK3 50859 Testican-3 precursor (SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 3). >AAACT m = 90 N = 61 n = 6 sig = 4.69688485008503 ENSG00000115446 UNC50 25972 unc-50 homolog ENSG00000118473 - 84251 SH3-domain GRB2-like (endophilin) interacting protein 1 ENSG00000156427 FGF18 8817 Fibroblast growth factor 18 precursor (FGF-18) (zFGF5). ENSG00000164651 SP8 221833...

16510498 http://sbi.imim.es/piana/ text/html; charset=unknown-8bit PIANA homepage: Protein Interactions And Network AnalysisStructural BioInformatics Research LabPeople  |  Research  |  Resources  |  Publications  |  Links  |    IMIMUPFGRIB SBI  PIANAProtein Interactions And Network Analysis     Attention! PIANA is not supported anymore. Check BIANA project instead...

...-308-S3.txt text/plain; charset=us-ascii Symbol Full Name A2LP ataxin 2 related protein A2M alpha-2-macroglobulin AADAC arylacetamide deacetylase (esterase) AAMP angio-associated, migratory cell protein AARS...lysophosphatidic acid acyltransferase, beta) AGR2 anterior gradient 2 (Xenepus laevis) homolog AGRP agouti (mouse) related protein AGTRL1 angiotensin receptor-like 1 AHCY S-adenosylhomocysteine hydrolase AHCYL1 S-adenosylhomocysteine hydrolase-like 1 AHR aryl hydrocarbon receptor AIF1 allograft inflammatory factor 1 AIM1 absent in melanoma 1 AIM2 absent in melanoma 2 AIP aryl hydrocarbon receptor-interacting protein AIP-1 abl-interactor 12 (SH3-containing protein) AIP4 atrophin-1 interacting protein 4 AK1 adenylate kinase 1 AK2 adenylate kinase 2 AK3...

...content/supplementary/1471-2105-5-100-S6.txt text/plain; charset=us-ascii YLR331C Jumonji Interacting Protein YLR332W Protein required for mating YLR333C ribosomal protein S25B (S31B) (rp45) (YS23) YLR333C ribosomal protein S25B (S31B) (rp45) (YS23) YLR334C Hypothetical ORF YLR335W nucleoporin YLR336C Suppressor of Glycerol Defect YLR337C proline-rich protein verprolin YLR338W Hypothetical ORF YLR339C Protein required for cell viability YLR295C ATP synthase subunit h YLR296W Hypothetical ORF YLR297W Hypothetical ORF...

...ServerThis is the web server BIPS (Biana Interolog Prediction Server). Here, you can predict putative interactions between proteins based on homologs found in Protein-Protein interaction databases. BIPS relies on data integrated in BIANA. You just need to insert your sequences of interest or list of protein identifiers, and BIPS will infer interactions based on homology. Predicted partners can be restricted to proteins added in your list or to the complete BIANA database. If you are unsure on...

...proteineupitrilysinexfoliatin Aexopeptidasefactor V activatorfalcilysinfalcipain-2falcipain-3family S24 unassigned peptidasesfamily S26 non-peptidase homologuesfarnesylated-protein converting enzyme 1feline immunodeficiency virus retropepsinfibrinolytic peptidasefibroblast activation protein alpha subunitfibrolaseflavivirinFLIP proteinfoot-and-mouth disease...cruziTrypanosoma evansiVaccinia virusVibrio choleraewalleye dermal sarcoma virusXenopus laevisYarrowia lipolyticaYersinia pseudotuberculosisSubstratePlease select A kinase (PRKA) anchor protein 8-like aggrecan Insulin-like growth factor-binding protein 6 precursor integrin alpha 5 precursor parathyroid hormone preproprotein PC4 and SFRS1 interacting protein 1 isoform 2 poly (ADP-ribose) polymerase family, member 1 prolyl 4-hydroxylase, beta subunit precursor Pry1 Pry2 RAS p21 protein activator 1 isoform 1 secreted phosphoprotein 1 isoform a secreted phosphoprotein 1 isoform b serine...

...et al. 2015Received: 14 February 2015Accepted: 22 May 2015Published: 6 June 2015AbstractBackgroundDuring spliceosome assembly, protein-protein interactions (PPI) are sequentially formed and disrupted to accommodate the spatial requirements of pre-mRNA substrate recognition and catalysis. Splicing activators and repressors, such as SR proteins and hnRNPs, modulate spliceosome assembly and regulate alternative splicing. However, it remains unclear how they differentially interact with the core spliceosome to perform their functions.ResultsHere, we investigate the protein connectivity of...

22067443 http://omics.bjcancer.org/pina/ text/html; charset=us-ascii PINA2PINA: Protein Interaction Network Analysis platform FeedbackContactLogin (free registration)    Home IntroductionStatistics & DownloadTutorialFAQ    Network Construction...Filter Filter (Annotation)Filter (GO similarity)    Network Analysis Network functionNetwork topologyTopologically important proteinsCommon interacting proteins    User Community Shared networks Shared comments    User Space My networks My commentsNetwork OperationIntroductionProtein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset...

...for many pathogens. However, many questions are relatively unexplored. What are the properties of human proteins that interact with pathogens? Do pathogens interact with certain functional classes of human proteins? Which infection mechanisms and pathways are commonly triggered by multiple pathogens? In this paper, we provide the first study of the landscape of human proteins interacting with pathogens. We integrate human-pathogen protein-protein interactions (PPIs) for 190 pathogen strains from seven public databases. Nearly all of the 10,477...

...PEP-SiteFinder/ text/html; charset=utf-8 PEP-SiteFinder PEP-SiteFinderA service to identify candidate protein-peptide interaction sites.OverviewWhy PEP-SiteFinder ?Run PEP-SiteFinderLatest newsPEP-SiteFinder' designWhat is PEP-SiteFinder not ?FeaturesLimitationsUsageInputResultsExamplesBenchmarkReferencesOverview Protein structure and peptide sequence to identify candidate sites of interactions on protein surface. Why PEP-SiteFinder ? The recent years have seen increased interest for peptides to probe molecular interactions, or for the early design of candidate therapeutics, which makes higly desirable the detailled caracterization...

...preg_match("/downloads.php/",$addr)) { echo " - Downloads"; } elseif(preg_match("/browse.php/",$addr)) { echo " - Browse Proteins"; } elseif(preg_match("/about.php/",$addr)) { echo " - About ENTS"; } ?> ENTSContact Us>Home>About>Browse>DownloadsHelpBatch Modebatch_mode_linkSpecify ProteinProtein: A Protein Name input_protein_name Cutoff: Min. Interaction confidence $i%"; } else { echo "$i%"; } } ?> select_cutoff Organism: Organism name MySQL error!"; } else $sql = "SELECT...

...HOMEOBOX) homolog [Homo sapiens] 2 . 5830416C07 unknown EST 2 157725694 6430402L23 similar to PUTATIVE RAB5-INTERACTING PROTEIN (DJ977B1.3.1) [Homo sapiens] 2 . 5830437K10 MODULATOR OF ANTIGEN RECEPTOR SIGNALING MARS 2 158056592 2610301H18 hypothetical protein 2 . 8430432F24 retinoblastoma-like 1 (p107) 2 158158725 1500001H18 ribophorin II 2 . 4930455J15 hypothetical protein 2 158436270 0710005O04 neuronatin 2 . 2610034M21 bladder cancer associated protein homolog (human) 2 158436251 NM_010923 Nnat 2 158956455 9430059M04 unclassifiable 2 . 2010009K17 unknown EST...

25792605 http://songyanglab.sysu.edu.cn/telopin/ text/html; charset=us-ascii TeloPIN: HomeTelomeric Proteins Interaction NetworkHomeProtein-ProteinBrowserStatistics and DownloadProtein-DNATeloChIP browserTelomeric Proteins ChIPTelomere-associated ProteinsStatistics and DownloadProtein-RNABrowserStatistics and DownloadProtein-DNA-RNABrowser and DownloadTutorial/ExamplesWelcome to TeloPIN DatabaseTelomeric Proteins Interaction Network(TeloPIN) Database is a collection of telomeric protein Protein-Protein Interaction (PPI), Protein-DNA Interaction and Protein-RNA Interaction data in mammalian cell from scientific literature and GEO database. The goal of database is...

...text/html; charset=us-ascii A Correlated Motif Approach for Finding Short Linear Motifs from Protein-Protein Interaction DataA Correlated Motif Approach for Finding Short Linear Motifs from Protein-Protein Interaction DataSoon Heng, Tan   Hugo Willy   Wing-Kin, Sung   See-Kiong, Ng An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments...

...http://caps.ncbs.res.in/peptidemine/ text/html; charset=utf-8 PeptideMine | Peptide Substrates from Interacting Proteins  Home ServerSearch & SubmitHelpGroupPeptideMine - WebServer for Identification and analysis of peptides from interacting proteins : PeptideMine is a webserver developed for identifying and analysing peptides suitable for protein-peptide binding studies. PeptideMine is using a unique, knowledge based approach for the identification of peptides from the interacting sequence-space of a protein using different search programs (PeptideMine Search, BLASTP and regular expression...

25348397 http://comppi.linkgroup.hu/ text/html; charset=us-ascii ComPPI - Main PageCompartmentalized Protein-Protein Interaction DatabaseHomeSearchDownloadsHelpTutorialContact UsWhat is ComPPI?Protein-protein interaction networks are spatially and temporally merged from the results of various experimental and predicting methods. These often ignore localization data, which in turn deteriorates the data quality and its predictive potential.We present ComPPI, the compartmentalized protein-protein interaction database, which provides qualitative information on the interactions, proteins and their localizations integrated from multiple...

21036873 http://www.megabionet.org/atpid/webfile/ text/html; charset=utf-8 AtPID AtPIDArabidopsis thaliana Protein Interactome DatabaseQUICK START:Please enter a single protein when you would like to know if some other protein can interact with it. Otherwise, enter a pair of protein to check if they can interact with each other according to our data collections and predictions. AtPID can identify a variety...

...bclab.inha.ac.kr/pridictor/ text/html; charset=utf-8 PRIdictor As many structures of protein-RNA complexes have been known in the past years, several computational methods have been developed...the past years, several computational methods have been developed to predict RNA-binding sites in protein. However, its inverse problem (i.e., predicting protein-binding sites in RNA) has received much less attention. Furthermore, most of the methods that predict RNA-binding sites in protein do not consider interaction partners (i.e., RNAs) of a protein, so they always predict the same binding sites for a given protein sequence even if...

...text/html; charset=utf-8 About - iRefWeb - Wodak LabAbout - iRefWeb - Wodak LabYou have:discovered a protein or a gene likely to be involved in a disease, and you want to find out what is known about its interactions with other proteins.identified a group of co-expressed genes, and would like to check if the proteins they code for interact physically.found a set of genes associated with a specific phenotype, or a cellular process...

...http://caps.ncbs.res.in/hori/ text/html; charset=utf-8 ..: HORI - Higher Order Residue Interactions in proteins :..  Home ServerHelpGroupHORI - Introduction:HORI - Higher Order Residue Interactions, is a web server to compute higher order interactions (pairwise interaction, triplet interactions and quadruple interactions) in a protein structure. HORI Server is available in three modules : HORI - Global, HORI - Lite and HORI - ClusterHORI...

...439P1ATF3Activating transcription factor 3467P1ATMAtaxia telangiectasia mutated (includes complementation groups A, C and D)472P1ATOX1ATX1 antioxidant protein 1 homolog (yeast)475P2ATRXAlpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)546P2ATXN3Ataxin 34287P2BACE1Beta-site APP-cleaving enzyme 123621P2BAK1BCL2-antagonist/killer 1578P1BAXBCL2-associated X protein581P1BCL2B-cell CLL/lymphoma 2596P1BIDBH3 interacting domain death agonist637P1BIKBCL2-interacting killer (apoptosis-inducing)638P1BIRC2Baculoviral IAP repeat-containing 2329P2BIRC3Baculoviral IAP repeat-containing 3330P1BIRC4Baculoviral IAP repeat-containing...

...-2105-9-8-S3.txt text/plain; charset=us-ascii >sp|Q9H3D4|P73L_HUMAN Tumor protein p73-like (p73L) (p63) (Tumor protein 63) (TP63) (p51) (p40) (Keratinocyte transcription factor KET) (Chronic...sp|Q16665|HIF1A_HUMAN Hypoxia-inducible factor 1 alpha (HIF-1 alpha) (HIF1 alpha) (ARNT- interacting protein) (Member of PAS protein 1) (MOP1) - Homo sapiens (Human). MEGAGGANDKKKISSERRKEKSRDAARSRRSKESEVFYELAHQLPLPHNVSSHLDKASVM RLTISYLRVRKLLDAGDLDIEDDMKAQMNCFYLKALDGFVMVLTDDGDMIYISDNVNKYM GLTQFELTGHSVFDFTHPCDHEEMREMLTHRNGLVKKGKEQNTQRSFFLRMKCTLTSRGR TMNIKSATWKVLHCTGHIHVYDTNSNQPQCGYKKPPMTCLVLICEPIPHPSNIEIPLDSK TFLSRHSLDMKFSYCDERITELMGYEPEELLGRSIYEYYHALDSDHLTKTHHDMFTKGQV TTGQYRMLAKRGGYVWVETQATVIYNTKNSQPQCIVCVNYVVSGIIQHDLIFSLQQTECV LKPVESSDMKMTQLFTKVESEDTSSLFDKLKKEPDALTLLAPAAGDTIISLDFGSNDTET DDQQLEEVPLYNDVMLPSPNEKLQNINLAMSPLPTAETPKPLRSSADPALNQEVALKLEP NPESLELSFTMPQIQDQTPSPSDGSTRQSSPEPNSPSEYCFYVDSDMVNEFKLELVEKLF AEDTEAKNPFSTQDTDLDLEMLAPYIPMDDDFQLRSFDQLSPLESSSASPESASPQSTVT VFQQTQIQEPTANATTTTATTDELKTVTKDRMEDIKILIASPSPTHIHKETTSATSSPYR DTQSRTASPNRAGKGVIEQTEKSHPRSPNVLSVALSQRTTVPEEELNPKILALQNAQRKR KMEHDGSLFQAVGIGTLLQQPDDHAATTSLSWKRVKGCKSSEQNGMEQKTIILIPSDLAC RLLGQSMDESGLPQLTSYDCEVNAPIQGSRNLLQGEELLRALDQVN >sp|P46060|RGP1_HUMAN Ran GTPase-activating protein 1 - Homo sapiens (Human). MASEDIAKLAETLAKTQVAGGQLSFKGKSLKLNTAEDAKDVIKEIEDFDSLEALRLEGNT VGVEAARVIAKALEKKSELKRCHWSDMFTGRLRTEIPPALISLGEGLITAGAQLVELDLS DNAFGPDGVQGFEALLKSSACFTLQELKLNNCGMGIGGGKILAAALTECHRKSSAQGKPL ALKVFVAGRNRLENDGATALAEAFRVIGTLEEVHMPQNGINHPGITALAQAFAVNPLLRV INLNDNTFTEKGAVAMAETLKTLRQVEVINFGDCLVRSKGAVAIADAIRGGLPKLKELNL SFCEIKRDAALAVAEAMADKAELEKLDLNGNTLGEEGCEQLQEVLEGFNMAKVLASLSDD EDEEEEEEGEEEEEEAEEEEEEDEEEEEEEEEEEEEEPQQRGQGEKSATPSRKILDPNTG EPAPVLSSPPPADVSTFLAFPSPEKLLRLGPKSSVLIAQQTDTSDPEKVVSAFLKVSSVF KDEATVRMAVQDAVDALMQKAFNSSSFNSNTFLTRLLVHMGLLKSEDKVKAIANLYGPLM ALNHMVQQDYFPKALAPLLLAFVTKPNSALESCSFARHSLLQTLYKV >sp...

...sinica.edu.tw/TMPad/ text/html; charset=us-ascii TMPadHomeSearchPDB ID:GoHomeHighlightSearchSearch ResultsBrowseStatisticsDownloadHelpFAQsAbout UsTMPadThe TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins. TMPad includes geometric descriptors of helix-helix interactions, topology, lipid accessibility, ligand and binding sites information.In addition, TMPad provides structural classification and...

...text/html; charset=us-ascii UsageOverview Biological processes are often performed by a group of proteins rather than by individual proteins, and proteins in a same biological group form a densely connected subgraph in a protein-protein interaction network. Therefore, finding a densely connected subgraph provides useful information to predict the function or protein complex of uncharacterized proteins in the highly connected subgraph. We have developed an efficient algorithm and program called ModuleSearch...

...Text:   Bulk SearchSequence Search  Accession NumberProtein NameNumber of Observed Peptidescathepsincathepsin1choline transporter-like protein 2choline transporter-like protein 22hexosaminidase-likehexosaminidase-like2hypothetical protein LOC321166hypothetical protein LOC3211661hypothetical protein LOC322814hypothetical protein LOC3228141hypothetical protein LOC324985hypothetical protein LOC3249852hypothetical...NumberProtein NameNumber of Observed Peptidescathepsincathepsin1choline transporter-like protein 2choline transporter-like protein 22hexosaminidase-likehexosaminidase-like2hypothetical protein LOC321166hypothetical protein LOC3211661hypothetical protein LOC322814hypothetical protein LOC3228141hypothetical protein LOC324985hypothetical protein LOC3249852hypothetical protein LOC336746hypothetical protein LOC3367461hypothetical protein LOC393175hypothetical...

...A,B,inhibitor), GO_term(B,'elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger') 9,1 SEP(A) :- drug_has_target(A,B...norfloxacin',HPCCchem) 8,1 SEP(A) :- drug_has_target(A,B,inhibitor), GO_term(B,'protein binding'), category(A,'Analgesics, Non-Narcotic') 8,1 SEP(A) :- drug_has_target(A,B,inhibitor), interact(B,C), pathway(C,'Pathogenic Escherichia coli infection',KEGG) 17,1 SEP(A) :- drug_has_target(A,B,activator), interact(B,C), interact(C,'Ankyrin-2') 5,0 SEP(A) :- drug_has_target(A,B,inhibitor), GO...

...apoptosis-related cysteine peptidase IL1R2 7850 Interleukin 1 receptor, type II MAP3K3 4215 Mitogen-activated protein kinase kinase kinase 3 DUSP8 1850 Dual specificity phosphatase 8 RAC3 5881 Ras-related C3...NLK 51701 Nemo-like kinase STMN1 3925 Stathmin 1/oncoprotein 18 MAPKAPK3 7867 Mitogen-activated protein kinase-activated protein kinase 3 CACNB3 784 Calcium channel, voltage-dependent, beta 3 subunit FGFR1 2260 Fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) MAP3K7IP2 23118 Mitogen-activated protein kinase kinase kinase 7 interacting protein 2 PPP3R1 5534 Protein phosphatase 3 (formerly 2B), regulatory subunit B, alpha isoform FGF2 2247 Fibroblast growth factor 2...

...html; charset=utf-8 iLoops ServeriLoops ServerSubmissionResultsHelpIntroduction (click to show/hide)The iLoops Server uses protein structural features (protein loops as classified in ArchDB and/or domains as classified in SCOP) to determine whether any pair of proteins interact or not. To do that, it uses data from both known protein interactions and putative non-interacting proteins (co-localized, non-redundant, non-interacting random protein pairs non-similar to PPIs), assigning positive and negative scores to the structural features.The...

...PredLast updated at 2015-12-07 06:13:08 Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeastShobhit Jain and Gary Bader MotivationMany intracellular signaling processes are mediated by interactions involving peptide recognition modules such as SH3 domains. These domains bind to small, linear protein sequence motifs which can be identified using high-throughput experimental screens such as phage display...

20947562 http://hintdb.hgc.jp/htp/ text/html; charset=us-ascii HitPredict - High confidence protein-protein interactionsHitPredictPHYSICAL PROTEIN-PROTEIN INTERACTIONS WITH RELIABILITY SCORESHome | Statistics | Download | Help  HitPredict is a resource of experimentally determined protein-protein interactions with reliability scores. Search interactions for a protein: All speciesH. sapiensM. musculusR. norvegicusA. thalianaD. melanogasterC. elegansC. jejuniS. cerevisiaeS. pombeE. coliH. pyloriP. falciparum Examples...

...html; charset=us-ascii Probabilistic Local WalksProbabilistic Local WalksAn Accurate And Efficient Method For Detecting Protein Complexes from Protein-Protein Interaction NetworksDownload this project as a .zip file Download this project as a tar.gz fileWhat is PLW?PLW (Probabilistic Local Walks) is a graph clustering algorithm, and was designed to detect protein complexes in protein-protein interaction (PPI) networks with high accuracy and efficiency.PLW uses a seed selection strategy to prioritise...

...Supplemental DataHomeAbout MePublicationsPresentationsMatthew DyerPhD Candidate - Virginia Bioinformatics InstituteSupplementary Data for "Computational Prediction of Host-Pathogen Protein-Protein Interactions"Authors:Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral Citation:Dyer, M. D., T. M. Murali, and B. W. Sobral. (2007). Computational prediction of host-pathogen protein-protein interactions. Bioinformatics 27:i159-i166. Description:We present a method that integrates known intra-species PPIs...

...www.csbio.sjtu.edu.cn/bioinf/IPMiner/ text/html; charset=utf-8 IPMiner: Hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction IPMiner: Hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction [Introduction]   [Code and...role in different biological processes, such as post-transcriptional gene regulation. It always functions through interacting with proteins. To understand the functions of ncRNAs, a fundamental step is to identify which protein interacts with this ncRNA. Therefore it is promising to computationally predict RNA-binding protein (RBP). In this study, we propose a computational method IPMiner to predict ncRNA-protein interactions...

...ServicesResearchTrainingIndustryAbout usPSICQUIC ViewExamples:BRCA2,Q06609,dmc1,10831611 Input FormBrowseHelpFeedbackInput Form > Browse 5,710,019 binary interactions found for search term *Service content: protein-proteinimportedspokeclusteredAPID InteractomesService content: protein-proteinimportedspokepredictedinternally-curatedBAR-104,854Service content: protein-proteinsmallmolecule-proteinnucleicacid-proteininternally-curatedimex curationmimix curationspokeevidencebhf-ucl-2,282Service content: protein-proteinsmallmolecule-proteinnucleicacid-proteinspokeclusteredBINDService content: smallmolecule-proteininternally-curatedevidencespokeexperimentally-observedBindingDBTimed outService content: protein-proteininternally-curatedrapid curationspokeevidenceBioGrid-1,371,394Service content: smallmolecule-proteininternally-curatedmimix curationspokeevidenceChEMBL-628,504Service content: protein...

...syringae] pv. tomato str. DC3000 Get selected INTERACTOMEIf you want to filter out inter-species interactions select "YES" and download againYESNO SearchOne protein name: Use Uniprot Name (e.g. "RASK_HUMAN"), UniProt AC (e.g. "P01116") or ENTREZ Gene Symbol (e.g. "KRAS")Select OrganismAll OrganismsHomo SapiensMus musculusCaenorhabditis elegansDrosophila melanogasterArabidopsis thalianaSaccharomyces cerevisiaeEscherichia coliExamples: HRAS, CCNA2_HUMAN, IL3RA , Q03330, SWI5_YEASTList of proteins (one per line):Use Uniprot Name (e.g. "RASK_HUMAN"), UniProt AC (e.g. "P01116...

...phase transitions that drive ribonucleoprotein granule assembly. In this paper, we report many PLDs in proteins associated with paraspeckles, subnuclear bodies that form around long noncoding RNA. We mapped the interactome network of paraspeckle proteins, finding enrichment of PLDs. We show that one protein, RBM14, connects key paraspeckle subcomplexes via interactions mediated by its PLD. We further show that the RBM14 PLD, as well as the...

...text/html; charset=us-ascii Apoptosis database HomeResearchMembersCoursesGrants and AwardsJobs and OpeningsExtending signalling pathways with protein-interaction networks. Application to apoptosis.Extending signalling pathways with protein-interaction networks. Application to apoptosis. Joan Planas-Iglesias, Emre Guney, Javier Garcia-Garcia, Kevin A. Robertson...present the supplementary materials and complete numerical results for the paper "Extending signalling pathways with protein-interaction networks. Application to apoptosis.". In this work, we build four different apoptotsis-related networks from the 53 hand-curated apoptotsis-related proteins known by 20051 (referred as seeds). These seeds are connected in networks according to the...

...and Drugs Online ResourcePlease enter your search below, or browse the list of drugs or proteins.About MATADORMATADOR is a resource for protein-chemical interactions. It differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interacton...

...usOverviewMembersFacilitiesGT Login (CSSB staff)Skolnick Research GroupPublicationsNews & EventsNewsDistinguished Lecture SeriesUpcoming SeminarsPast SeminarsSoftware & ServicesServicesSoftwareDatabasesSimulationsJobs APoc Most proteins interact with small-molecule ligands such as metabolites or drug compounds. Over the past several decades, many of these interactions have been captured in high-resolution atomic structures. From a geometric point of view, most interaction sites for grasping these small-molecule ligands, as revealed in these structures, form concave shapes...

27208273 http://netbio.sjtu.edu.cn/arappinet/ text/html; charset=us-ascii Welcome to AraPPINetAraPPINet - Protein-Protein Interaction Network for Arabidopsis The global Arabidopsis PPI network (AraPPINet) that was inferred from both three-dimensional structures and functional evidence and that encompasses 316,747 high-confidence interactions among 12,574 proteins(download arappinet full dataset). AraPPINet exhibited high predictive power for discovering protein interactions at a 50% true positive rate and for discriminating positive interactions from similar protein pairs...

...narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.Bulk linking to third party resources by using involved proteinsProteins by Reactome pathway: Sends your proteins to the Reactome SkyPainter that will show you the pathways in which these molecules are know to play a role. Proteins by Chromosomal location: Sends your list of proteins to Ensembl’s Karyotype viewer and...

...IP/MS-2-PPI-DDIHomeComplexesPPIDDINavigationAboutDownloads    Data and Tables    FiguresAboutCoregulator proteins (CoRegs) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin...lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between...

...caps.ncbs.res.in/dockscore/ text/html; charset=us-ascii DockScore - a webserver for ranking protein-protein docked posesDOCKSCORE: a webserver for ranking protein-protein docked posesHome | Help | Methods | Example Run | GroupDOCKSCORE: a webserver for ranking protein-protein docked poses Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small...

...UbiNet UbiNet is a knowledge-based system that could provide potential E3 ligases for ubiquitinated proteins by the information of protein-protein interactions and substrate site specificities. In eukaryotes, protein ubiquitination catalyzed by E3 ubiquitin ligases plays crucial roles in regulating a variety of biological...there exists no resource designed to explore the regulatory networks of E3 ligases for ubiquitinated proteins in humans. Therefore, the UbiNet was designed to provide a full investigation of protein ubiquitination networks by integrating all available ubiquitinome datasets, experimentally verified E3 ligases, and protein-protein interactions. Moreover, UbiNet could provide potential E3 ligases for ubiquitinated proteins by the information of protein...

...ANCHOR?ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein-protein interfaces with regard to its suitability for small molecule drug design.ANCHOR visualization toolThe idea behind itSmall molecule inhibitors of protein-protein interactions often bind to the hotspot areas at the protein-protein interface. The identification of hotspots residues thus constitute valuable information to be exploited on the...

25892709 http://digbio.missouri.edu/IEW/index.html text/plain; charset=us-ascii Essential Protein Identification Based on Essential Protein-Protein Interaction Prediction by Integrated Edge WeightsEssential Protein Identification Based on Essential Protein-Protein Interaction Prediction by Integrated Edge Weights[Introduction][Workflow][Result][Script]1. IntroductionIntegrated Edge Weights (IEW) is a novel computational method to identify essential proteins. It works by ranking protein-protein interactions according to their integrated edge weights first, and then identified sub PPI networks consisting...