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 16

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

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

genome functional registered omim comparative kendall's homology
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

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Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

pdb obligatory same psi-blast solvent residue
The RCSB PDB information portal for structural genomics.

PMID 16381872 · PMC1347482 · Nucleic acids research · 2006 · 7 claims · 5 setups

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The RCSB PDB Structural Genomics Information Portal integrates three resources: Structural Genomics Initiatives, Targets (TargetDB/PepcDB), and Structures (functional coverage analysis).

structural nih genome sequence target production
MODBASE, a database of annotated comparative protein structure models and associated resources.

PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

sequences chains template chain comparative pairwise ligand
A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

PMID 19958498 · PMC2788387 · BMC genomics · 2009 · 8 claims · 4 setups

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Comparative homology modeling of wild-type and mutant α-mannosidase across human, cow, cat and guinea pig reveals a significant correlation between genotype severity and phenotype severity in α-mannosidosis

lysosomal full-length pro-peptide bovine homology sequence weblogo
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

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TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

scop-derived malt nr-70 scop profile-based dali remote
Coverage of whole proteome by structural genomics observed through protein homology modeling database.

PMID 17146617 · PMC1769342 · Journal of structural and functional genomics · 2006 · 8 claims · 7 setups

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FAMSBASE, a homology-modeling database of whole-genome ORFs, currently covers about 50% of predicted ORFs (368,724 of 734,193) across 276 genomes with modeled 3D structures.

orfs predicted modeled representative homology transmembrane intrinsic
Evolutionary history of the UCP gene family: gene duplication and selection.

PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

vertebrate ucp human-mouse ucp1 sequence phylogenetic gene
Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

PMID 33253310 · PMC7738170 · PLoS pathogens · 2020 · 7 claims · 8 setups

Has reproduction · 98

Non-synonymous mutations in dnaA are statistically associated with drug resistance (INH, RIF, SM) in clinical M. tuberculosis strains across two independent GWAS cohorts (China and Vietnam)

clinical dnaa isogenic h37rv genome-wide structural deep-sequencing
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
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

PMID 16630345 · PMC1489951 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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Sequence conservation (PSIC score difference) at the nsSNP position is the single most useful attribute for predicting deleterious vs neutral status.

swissprot nssnp-containing nssnps machine single-attribute sequence
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
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
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

Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

The RCSB PDB information portal for structural genomics.

MODBASE, a database of annotated comparative protein structure models and associated resources.

A multi-species comparative structural bioinformatics analysis of inherited mutations in alpha-D-mannosidase reveals strong genotype-phenotype correlation.

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

Coverage of whole proteome by structural genomics observed through protein homology modeling database.

Evolutionary history of the UCP gene family: gene duplication and selection.

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis.

Natural history of S-adenosylmethionine-binding proteins.

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes.

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

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.

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.