The papers in relatedwork/ are a work list, not background reading

The papers in related_work/ are a work list, not background reading

A supplied paper is not context. It names the tools the field uses on this problem, the benchmark events results are reported against, the baselines a number is compared to. Those names are what a reader checks your work for, and they are sitting in a file you already have.

The failure this prevents

It is not that runs skip the papers. Measured across a 40-task batch: every task ships them (median 4 PDFs, median 250,000 characters of extractable text) and every run referenced 100% of them. They are opened. They are read for framing. Then the work list is written from the task statement alone, and everything the papers name goes unused.

Chemistry_002 is the clean case. CAPRI appears 30 times in its supplied papers and HADDOCK3 22 times. The two graded requirements that name them — a CAPRI round result, and the tool's consensus scoring workflow — scored 5 and 0. The report discusses CAPRI as a concept and never reports a CAPRI result. Life_001's papers name NetMHCpan five times; the requirement naming it scored 5.

The shape is always the same: the run knows the field's vocabulary, because it read the papers, and produces its own analysis in its own terms beside a literature it has paraphrased rather than used.

What to do

1. While the papers are open at literature stage, write literature/named_from_papers.json: one row per proper noun the supplied papers attach to a result — a tool (HADDOCK3), a benchmark or event (CAPRI round 57), a dataset, a metric with a name, a scoring function, a public baseline. Carry the paper it came from and how many times it appears; something named twenty times is load-bearing and something named once may not be.
2. For each row decide, in writing, one of three things: run it, compare against it, or say why not — the tool is unavailable, the event has no public data, the dataset needs an account. Undecided is not one of the three.
3. Use the source's name in your section heading and in the prose. "We evaluate with HADDOCK3's consensus scoring" is checkable; "we use a modular scoring workflow" is the same work, unfindable.
4. Report the named quantity in the named units on the named benchmark. A run that computes the right thing and reports it against its own private split has not made the