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).

• Prediction of specificity-determining residues for small-molecule kinase inhibitors.

  PMID 19032760 · PMC2655090 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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  S-Filter is a novel method combining sequence and structural information (within PFAAT) to predict specificity-determining residues and selectivity profiles for small-molecule kinase inhibitors

  panel kinase-inhibitor sequence erk2 caliper radiometric solvent

• 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

• Genome bioinformatic analysis of nonsynonymous SNPs.

  PMID 17708757 · PMC1978506 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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  Structure- and sequence-based prediction tools can generally distinguish disease-causing mutations from neutral ones

  gene modelled nssnps automated fold relative

• Prodepth: predict residue depth by support vector regression approach from protein sequences only.

  PMID 19759917 · PMC2742725 · PloS one · 2009 · 8 claims · 8 setups

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  Residue depth can be reliably predicted solely from protein primary sequence using support vector regression on sequence-derived features.

  structure sequences sequence residue dssp psi-blast

• 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

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• 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

• 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

• Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.

  PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups

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  The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues

  benchmarking same pirsf pdb supervised wrapper sequence

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

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  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• 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

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• Structural evolution of the protein kinase-like superfamily.

  PMID 16244704 · PMC1261164 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  All kinases in the superfamily share a 'universal core' domain consisting only of the regions required for ATP binding and the phosphotransfer reaction.

  bank representative same kinase comparative manual structure-annotated