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DOMINE: a database of protein domain interactions

Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, Raja Jothi
2007 Nucleic Acids Research  
DOMINE is a database of known and predicted protein domain interactions compiled from a variety of sources.  ...  This database will serve as a valuable resource to those working in the field of protein and domain interactions.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkm761 pmid:17913741 pmcid:PMC2238965 fatcat:zayfjpmhkvgy3e53rgiqeoxcbu

Sequence-based prediction of function site and protein-ligand interaction by a functionally annotated domain profile database [article]

Dengming Ming, Min Han, Xiongbo An
2017 arXiv   pre-print
The key of the method hinges on a function- and interaction-annotated protein domain profile database, called fiDPD, which was built from the Structural Classification of Proteins (SCOP) database, using  ...  In this study, we have presented a new method for prediction of PLIs and PFSs based on sequence of the inquiry protein.  ...  Very recently, we applied FDPA to all available protein domain structures recorded in structural classification of protein database (SCOP) [49] , and created a functionally annotated domain profile database  ... 
arXiv:1701.08086v1 fatcat:fw4kyd5nhbhd5gfnvnvme5ebvi

Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database

Min Han, Yifan Song, Jiaqiang Qian, Dengming Ming
2018 BMC Bioinformatics  
The method is based on a functional site and physicochemical interaction-annotated domain profile database, called fiDPD, which was built using protein domains found in the Protein Data Bank.  ...  Results: In this paper, we present a sequence-based method for the prediction of physicochemical interactions at PFSs.  ...  Acknowledgements This work began when one of the author (DM) visited CNLS in Los Alamos National Laboratory. DM thanks Michael Wall for helpful discussions in early days of this work.  ... 
doi:10.1186/s12859-018-2206-2 pmid:29859055 pmcid:PMC5984826 fatcat:peq6reiy4nhexfreukcfa5j6a4

Dominant-NegativeGCMBMutations Cause an Autosomal Dominant Form of Hypoparathyroidism

Michael Mannstadt, Guylène Bertrand, Mihaela Muresan, Georges Weryha, Bruno Leheup, Sirish R. Pulusani, Bernard Grandchamp, Harald Jüppner, Caroline Silve
2008 Journal of Clinical Endocrinology and Metabolism  
The mutant GCMB proteins were well expressed, and both showed dose-dependent inhibition of the transactivation capacity of wild-type protein in luciferase reporter assays.  ...  Heterozygous mutations in pre-pro-PTH or the calcium-sensing receptor (CaSR) cause some forms of autosomal dominant HP (AD-HP).  ...  of the wild-type protein and whether an interaction with cofactors is altered or disrupted.  ... 
doi:10.1210/jc.2007-2167 pmid:18583467 pmcid:PMC2567849 fatcat:tshassigwrfgzhvcw3lxtniy3y

Dominating Biological Networks

Tijana Milenković, Vesna Memišević, Anthony Bonato, Nataša Pržulj, Franca Fraternali
2011 PLoS ONE  
Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS.  ...  Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology.  ...  HIV genes (HIV) are human genes known to interact with genes of the HIV virus [63] that are available from HIV-1-Human Protein Interaction Database (http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions  ... 
doi:10.1371/journal.pone.0023016 pmid:21887225 pmcid:PMC3162560 fatcat:4jwmk67hrjh53osfvygmnclyky

PKD1 (polycystic kidney disease 1 (autosomal dominant))

YC Tan, H Rennert
2012 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
The short intracellular C-terminal region has 197 aa, containing a coiled-coil domain that interact with polycystin-2 and a G-protein binding domain.  ...  Protein structure of polycystin-1 (PC1). The details of the protein domain structures are shown.  ...  PKD1 (polycystic kidney disease 1 (autosomal dominant)). Atlas Genet Cytogenet Oncol Haematol. 2012; 16(1):22-24.  ... 
doi:10.4267/2042/47263 fatcat:q4yabcidhfcqbedoz26mrgqqpe

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

Sailu Yellaboina, Asba Tasneem, Dmitri V. Zaykin, Balaji Raghavachari, Raja Jothi
2010 Nucleic Acids Research  
DOMINE will serve as a valuable resource to those studying protein and domain interactions.  ...  DOMINE is a comprehensive collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq1229 pmid:21113022 pmcid:PMC3013741 fatcat:7thprdvunnfdrfbcqhigcjfxju

Dominant collagen XII mutations cause a distal myopathy

Payam Mohassel, Teerin Liewluck, Ying Hu, Daniel Ezzo, Tracy Ogata, Dimah Saade, Sarah Neuhaus, Véronique Bolduc, Yaqun Zou, Sandra Donkervoort, Livija Medne, Charlotte J. Sumner (+10 others)
2019 Annals of Clinical and Translational Neurology  
To characterize the natural history and clinical features of myopathies caused by mono-allelic, dominantly acting pathogenic variants in COL12A1.  ...  A full list of contributing groups can be found at http://exac.broadinstitute.org/about. Conflict of Interest The authors do not have any relevant financial conflicts of interest.  ...  However, the bulky missense variant in the N-terminal Col2 domain then de-stabilizes the three-dimensional structure of the homotrimer or disrupts its protein-protein interactions with fibrillar collagen  ... 
doi:10.1002/acn3.50882 pmid:31509352 pmcid:PMC6801183 fatcat:keisbd2x5nc4vaim2dntb7wtdu

One-component systems dominate signal transduction in prokaryotes

Luke E. Ulrich, Eugene V. Koonin, Igor B. Zhulin
2005 Trends in Microbiology  
By analyzing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer  ...  domains typical of two-component systems.  ...  We also acknowledge the valuable work of the Pfam, SMART and COG developers.  ... 
doi:10.1016/j.tim.2004.12.006 pmid:15680762 pmcid:PMC2756188 fatcat:gjrfkwayzrhb3cz4lxjrrmugka

Mutation inCPT1CAssociated With Pure Autosomal Dominant Spastic Paraplegia

Carlo Rinaldi, Thomas Schmidt, Alan J. Situ, Janel O. Johnson, Philip R. Lee, Ke-lian Chen, Laura C. Bott, Rut Fadó, George H. Harmison, Sara Parodi, Christopher Grunseich, Benoît Renvoisé (+12 others)
2015 JAMA Neurology  
Nevertheless, a genetic diagnosis remains unavailable for many patients. OBJECTIVE To identify the genetic cause for a novel form of pure autosomal dominant HSP.  ...  We showed that CPT1C, which localizes to the endoplasmic reticulum, is expressed in motor neurons and interacts with atlastin-1, an endoplasmic reticulum protein encoded by the ATL1 gene known to be mutated  ...  NMR Spectroscopy The regulatory domain of human CPT1C (Met1-Phe50), the N domain, incorporated the Arg37Cys substitution and was produced as a fusion to the third IgG-binding domain of protein G within  ... 
doi:10.1001/jamaneurol.2014.4769 pmid:25751282 pmcid:PMC5612424 fatcat:avh6mpljkndzvjxvsaub4yebsy

TBC1D24Mutation Causes Autosomal-Dominant Nonsyndromic Hearing Loss

Hela Azaiez, Kevin T. Booth, Fengxiao Bu, Patrick Huygen, Seiji B. Shibata, A. Eliot Shearer, Diana Kolbe, Nicole Meyer, E. Ann Black-Ziegelbein, Richard J.H. Smith
2014 Human Mutation  
TBC1D24 encodes a GTPase-activating protein expressed in the cochlea. Ser178 is highly conserved across vertebrates and its change is predicted to be damaging.  ...  , mental retardation and seizures (DOORS syndrome), and a wide range of epileptic disorders.  ...  TBC1D24 encodes a protein with two conserved domains: a TBC domain (tre2/Bub2/ Cdc16), which is shared by Rab GTPase-activating proteins (Rab-GTPs); and a TLDc domain, which is believed to be involved  ... 
doi:10.1002/humu.22557 pmid:24729539 pmcid:PMC4267685 fatcat:5hchruhgnbeofmyhd5jh4jrsum

ALDH18A1gene mutations cause dominant spastic paraplegia SPG9: loss of function effect and plausibility of a dominant negative mechanism

Emanuele Panza, Juan M. Escamilla-Honrubia, Clara Marco-Marín, Nadine Gougeard, Giuseppe De Michele, Vincenzo Brescia Morra, Rocco Liguori, Leonardo Salviati, Maria Alice Donati, Roberto Cusano, Tommaso Pippucci, Roberto Ravazzolo (+7 others)
2015 Brain  
ALDH18A1 gene mutations cause dominant spastic paraplegia SPG9: loss of function effect and plausibility of a dominant negative mechanism. Brain 139(1): e3.  ...  of this human domain at the domain surface, as required for domain-domain interacting residues, each one quite close to the other.  ...  In fact, the E. coli G5K residues corresponding to three of these four dominant mutation-hosting residues of the human G5K domain are involved in the interactions with other subunits or domains of the  ... 
doi:10.1093/brain/awv247 pmid:26297558 fatcat:hnl6hu6hubc4hd44gqqdruf7k4

Autosomal Dominant Polycystic Kidney Disease: At a Glance

Parimal Das
2018 Public Health Open Access  
Polycystic kidney disease (PKD) is a systemic disorder which adds majority of renal patients to end stage renal disease (ESRD).  ...  Among all type of PKD, autosomal dominant polycystic kidney disease (ADPKD) is most prevalent and fourth most leading cause of dialysis and kidney transplant.  ...  PC1 encoded by PKD1 is cardinal member of a novel class of proteins involved in developmental processes [44] . PC1 has evolutionary conserved domains of multiple functions [45] .  ... 
doi:10.23880/phoa-16000126 fatcat:yxskbnplvvd25bgky23c3rskcu

Novel LDB3 Mutation in a Patient With Autosomal Dominant Myofibrillar Myopathy

Farah Talebi, Farideh Ghanbari, Javad Mohammadi Asl
2016 Gene Cell and Tissue  
LDB3 protein encoded by this gene is a key Z-disk protein that interacts with α-actinin and protein kinase C.  ...  Case Presentation: In this paper, we identified the novel heterozygous, and hence, dominant mutation in the LIM domain-binding protein 3 gene (LDB3) in a patient affected by myofibrillar myopathy (MFM)  ...  PDZ domain-containing proteins interact with a number of proteins involved in clustering and targeting of membrane proteins or with each other in cytoskeletal assembly.  ... 
doi:10.17795/gct-34601 fatcat:4kwqqgue2vhtdppxnrjym2esua

Mutations of DEPDC5 cause autosomal dominant focal epilepsies

Saeko Ishida, Fabienne Picard, Gabrielle Rudolf, Eric Noé, Guillaume Achaz, Pierre Thomas, Pierre Genton, Emeline Mundwiller, Markus Wolff, Christian Marescaux, Richard Miles, Michel Baulac (+3 others)
2013 Nature Genetics  
S.I received a grant of the French Government. This study was supported by the program "Investissements d'avenir" ANR-10-IAIHU-06.  ...  Acknowledgments We thank the genotyping and sequencing platform of ICM for technical assistance, the DNA and cell bank of ICM for DNA extraction and cell culture, Philippe Couarch for technical assistance  ...  The presence of a DEP domain (Dishevelled, Egl-10 and Pleckstrin domain), a globular protein motif of about 80 amino acids present in many proteins of G-protein signaling pathways, suggests this gene may  ... 
doi:10.1038/ng.2601 pmid:23542701 pmcid:PMC5010101 fatcat:lqctpw2u6jfofpprauwhc3emj4
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