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 31

System / cell line: mutant ✕ Assay: molecular ✕ Clear

Solving structures of protein complexes by molecular replacement with Phaser.

PMID 17164524 · PMC2483468 · Acta crystallographica. Section D, Biological crystallography · 2007 · 7 claims · 4 setups

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Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components using a 'tree search with pruning' approach implemented in Phaser's automated MR mode.

β-lactamase rop antibody ap2 molecular
Functional analysis of human mutations in homeodomain transcription factor PITX3.

PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

lens western immunocytochemistry electrophoretic
Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

PMID 18546365 · PMC2891192 · Human mutation · 2008 · 8 claims · 4 setups

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POLG mutations cause at least 6 major heterogeneous phenotypes of neurodegenerative mitochondrial disease (MCHS, Alpers syndrome, ANS, MEMSA, arPEO, adPEO)

blood parental model sanger parental microsatellite
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
What have we learned from the congenital myasthenic syndromes.

PMID 19688192 · PMC3050586 · Journal of molecular neuroscience : MN · 2010 · 8 claims · 8 setups

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CMS have been traced to mutations in at least 11 disease genes encoding proteins at the neuromuscular junction

endplate endplates cos bacterially electron intracellular density
Molecular dynamics and mutational analysis of a channelopathy mutation in the IIS6 helix of Ca V 1.2.

PMID 18836301 · PMC3196984 · Channels (Austin, Tex.) · 2008 · 8 claims · 4 setups

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I781T in CaV1.2 shifts the voltage-dependence of activation and inactivation to hyperpolarized voltages, reproducing the channelopathy-like gating phenotype of CaV1.4 I745T

homology tsa-201 cav1.2 molecular whole-cell confocal
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
A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

PMID 19668596 · PMC2722711 · Molecular vision · 2009 · 8 claims · 6 setups

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A novel heterozygous CRYGD mutation c.43C>A (R15S) causes congenital coralliform cataract in Family A

family genomic crygd lens two-point microsatellite direct
Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

PMID 16989739 · PMC3933161 · Journal of cellular and molecular medicine · 2006 · 6 claims · 8 setups

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Mutations in APP, PS1 and PS2 genes and polymorphisms in the APOE gene are implicated in AD pathogenesis

alzheimer brain alzheimer's presenilin-1 microarray proteomic transgenic
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
Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

PMID 15719063 · PMC548953 · PLoS biology · 2005 · 8 claims · 3 setups

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Discovery-based genomics research can be integrated into an undergraduate curriculum, engaging large numbers of students in professional-quality research without compromising didactic training

drosophila genomic flp p-element molecular
Microarray analysis: genome-scale hypothesis scanning.

PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

drosophila yeast diffuse breast microarray integrated gene
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

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The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

recombinant cyp2d6 computational resonance uv-vis sds-page
ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups

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Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI

clinical gonorrhoeae coli mic spontaneous pcr
Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular
CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

PMID 41056017 · PMC12646653 · The Journal of clinical investigation · 2025 · 8 claims · 8 setups

Has reproduction · 67

Heterozygous CDKL1 missense variants (Cys143Arg, Ser206Leu, Thr135Met) were identified in 6 patients from 3 families with TAAD spectrum disorders

patients cohort cdkl1 aortic exome gene structural
Multiplexed genetic analysis using an expanded genetic alphabet.

PMID 15319316 · PMC1592527 · Clinical chemistry · 2004 · 7 claims · 6 setups

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MultiCode PLx is a three-step platform (PCR, target-specific extension, liquid chip decoding) performed in a single reaction vessel and completed in ~3 h

genomic synthetic subset newborn multicode eracode automated
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
Adapting to a changing world: RAG genomics and evolution.

PMID 16004728 · PMC3525258 · Human genomics · 2005 · 8 claims · 7 setups

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RAG-1/RAG-2 origin is a foundational hallmark of adaptive immunity, enabling V(D)J recombination of antigen receptor genes.

rag-1 patients zebrafish vertebrate comparative site-directed clinical
Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

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50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

genomic α-gal cos-7 transcripts pcr southern microsatellite

Experiments

Solving structures of protein complexes by molecular replacement with Phaser.

Functional analysis of human mutations in homeodomain transcription factor PITX3.

Molecular and clinical genetics of mitochondrial diseases due to POLG mutations.

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

What have we learned from the congenital myasthenic syndromes.

Molecular dynamics and mutational analysis of a channelopathy mutation in the IIS6 helix of Ca V 1.2.

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

A novel gammaD-crystallin mutation causes mild changes in protein properties but leads to congenital coralliform cataract.

Synaptic dysfunction and oxidative stress in Alzheimer's disease: emerging mechanisms.

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

Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers.

Microarray analysis: genome-scale hypothesis scanning.

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.

Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

Multiplexed genetic analysis using an expanded genetic alphabet.

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

Adapting to a changing world: RAG genomics and evolution.

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.