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).

• Predicting the pathogenicity of missense variants using features derived from AlphaFold2.

  PMID 37084271 · PMC10203375 · Bioinformatics (Oxford, England) · 2023 · 6 claims · 8 setups

  Has reproduction · 85

  AlphaFold2-derived structural features (solvent accessibility, amino acid network features, physicochemical environment, pLDDT) can be used to train a random forest classifier (AlphScore) that distinguishes proxy-benign from proxy-pathogenic missense variants.

  gnomad alphafold2-predicted alphscore proteins machine secondary physicochemical

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

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

  Full-text index only

  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

• 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

• 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

• 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 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

• 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