Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 18

System / cell line: crystal ✕ Assay: homology ✕ Clear

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

PMID 19714203 · PMC2722018 · PLoS computational biology · 2009 · 8 claims · 8 setups

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Cancer mutations in ABL and EGFR activate kinases via a common multi-stage mechanism involving hydrophobic spine assembly, formation of a Src-like intermediate structure, and cooperative breakage/formation of characteristic salt bridges

abl egfr abl-sh2-sh3 homology molecular stability
Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

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Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

ceacam1 meningitidis influenzae ha3 homology site-directed receptor
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

PMID 16646632 · PMC1450327 · PLoS biology · 2006 · 8 claims · 5 setups

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The C-terminal domain of the gE ectodomain (CgE) is the minimal Fc-binding domain of gE-gI

recombinant selenomethionine-substituted ge-gi models surface x-ray computational
Conservation, variability and the modeling of active protein kinases.

PMID 17912359 · PMC1989141 · PloS one · 2007 · 7 claims · 5 setups

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A novel sequence-order independent (fold-independent) structural alignment algorithm was developed that maximizes side-chain similarity to produce a consensus kinase structure.

active-conformation same chak rio2 sequence-order pairwise structural
Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

PMID 15757514 · PMC1084347 · BMC microbiology · 2005 · 8 claims · 7 setups

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PSI-BLAST identified several novel homologies between LEE-encoded and Ysc-Yop-associated proteins

lee-encoded escc sepq escd psi-blast blastp domain
A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

PMID 18618005 · PMC2447816 · Molecular vision · 2008 · 6 claims · 4 setups

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A heterozygous c.327C>A transversion in exon 3 of CRYGC causes a nonsense mutation (C109X) that cosegregates with autosomal dominant congenital nuclear cataract in a Chinese family.

genomic type family γc-crystallin pcr comparative clinical
The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

PMID 14519199 · PMC328453 · Genome biology · 2003 · 8 claims · 5 setups

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Sequence-profile (PSI-BLAST) searches unify archaeal Alba with eukaryotic RNase P/MRP subunits Rpp20/Pop7 and Rpp25, and with the ciliate macronuclear-development protein Mdp2, into a single Alba superfamily.

archaeal eukaryotic alba sulfolobus psi-blast sequence phylogenetic
Natural history of S-adenosylmethionine-binding proteins.

PMID 16225687 · PMC1282579 · BMC structural biology · 2005 · 8 claims · 6 setups

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The last universal common ancestor (LUCA) of cellular life had between 10 and 20 SAM-binding proteins from at least 5 fold classes

arabidopsis nicotianamine rossmann-fold cyclopropane psi-blast pdbblast comparative
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

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The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

genomic retina cdna protocadherin str pcr rt-pcr
Crystallin gene mutations in Indian families with inherited pediatric cataract.

PMID 18587492 · PMC2435160 · Molecular vision · 2008 · 8 claims · 5 setups

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Crystallin gene mutations account for 16.6% of inherited pediatric cataract in this south Indian population

genomic pcr affected pediatric single direct restriction
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

natural aligned ns3 denv sequence pcp-consensus physicochemical
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

scientific pubmed cyp-drug cyp text mutation manual
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification

Experiments

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.

Conservation, variability and the modeling of active protein kinases.

Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion.

A nonsense mutation in CRYGC associated with autosomal dominant congenital nuclear cataract in a Chinese family.

The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism.

Natural history of S-adenosylmethionine-binding proteins.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

Crystallin gene mutations in Indian families with inherited pediatric cataract.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.