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DOMINE: a database of protein domain interactions
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]
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
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
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
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))
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
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
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
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
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
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
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
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
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
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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