blog · category
7 articles on protein science, newest first.
the log
7 articles · Protein Science
all articleslatest article · Protein Science
A computational developability screen is a triage instrument, not a substitute for the panel. Sequence-motif liability flags have published grading against forced degradation; composite developability scores correlate with the measured assays at |rho| of about 0.3 or less. Here is what each half of the comparison actually supports.
· 18 min read
ProteinMPNN recovers 52.4% of native residues against Rosetta's 32.9%. That figure is a benchmark on solved backbones, not a success rate — here is what it does predict, what it cannot, and what to measure instead.
P2Rank scores points on a protein's surface with a random forest; fpocket clusters alpha spheres found by Voronoi tessellation. P2Rank ranks the true site higher, fpocket finds more sites somewhere in a longer list, and the best published configuration is fpocket's pockets re-ranked by P2Rank's own scorer. How the two methods work, what the benchmarks actually measured, and which to reach for.
Plain BLAST settles most homology questions, and it stops working in the twilight zone below about 30% identity. A practical comparison of pairwise BLAST, iterated PSI-BLAST and profile-HMM search with HMMER: what each detects, what each gets wrong, and how to choose.
Pocket predictors such as P2Rank work on AlphaFold and ESMFold models, but a predicted pocket is only as trustworthy as the residues lining it. Here is what changes between predicted and experimental structures, which P2Rank model to use, how to read pocket scores, and how the fold → pocket → dock pipeline runs on .bloom*.
Germline identity, a gene-specific CNN classifier and a 9-mer repertoire search all answer "how human is this antibody?" — about different objects, on different scales, with different blind spots. What each score measures, where they disagree, and what none of them predicts.
A practical comparison of ESMFold and AlphaFold2 for drug discovery — covering accuracy, speed, when to use each, and how to run both on the Ivy Biosciences platform.
newsletter
