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Part IV of Molecular Docking in the AI Era covers software that changes faster than a book can be reprinted. This page carries the current state and a dated record of what has moved, so that a chapter written in 2026 stays usable.

Where this page and the book disagree, this page is current and the book records what was true when it was checked. Checked is the date someone last read the upstream source, not the date the version was released: a row checked long ago is a row you should verify yourself.

How these were checked

Every value below was read from the project's own repository, release page or licence file. No summary site, package-tracker or blog post was used, because those are exactly the sources that go stale without saying so. The Source column is the page actually read, so you can repeat the check rather than trust it.

Where a value could not be found, the row says not found and where the search was made. Where two primary sources disagree, both are recorded.

Tools

An em dash in the second column means the repository does not pin that tool. smina, GNINA, PLIP and GROMACS appear in the book's prose but are not part of the pinned environment, so there is no version for them to be measured against. The other seven are pinned, and requirements.txt is authoritative for them: six carry an exact == pin there and can each move a number the book prints. Open Babel is the seventh, pinned by the instructions in that file rather than by a line pip can install, because the version you get depends on your platform.

Two dates are given for RDKit because its GitHub release and its PyPI upload are five days apart. Same version, different publication events; neither is wrong. gemmi and NumPy were read from PyPI, which is where the pinned artefact actually comes from. Open Babel 3.2.1 is current upstream but is still not what most package managers install, which is why the book's column names both numbers.

smina is the one row with no version, because it publishes no versioned release at all. Its SourceForge files page carries dated binaries rather than releases: the newest is smina.osx.12, dated 2021-12-01, and the Linux smina.static build is dated 2019-10-15. The GitHub mirror has no tags and its last commit is 2018-11-18. A date is the most precise thing that can honestly be recorded.

GROMACS maintains more than one branch at a time, so the newest release is not always the newest upload: 2025.5 was published on 2026-08-31, after 2026.3.

A pin sitting behind the current release is the expected state, not a defect. The pins reproduce the book's numbers; upgrading is what changes them. The build record lists the differences already found and what caused them.

Models and their terms

Each licence below was read from the project's own LICENSE file or terms document, not from a third party's description of it.

The AlphaFold 3 weights are the one entry where two documents have to be read together. The Terms of Use, still marked Last Modified: 2024-11-09, restrict the parameters to “non-commercial use by, or on behalf of, non-commercial organizations”; the Prohibited Use Policy adds that those organisations may use them only for their non-commercial activities. Both tests must be met, and a commercial organisation is excluded even when the work is non-commercial. What changed in 2026 was not who may use the weights but how they are obtained: the request form was removed on 2026-07-23 and the download is now public. The chapters were corrected before printing.

Chapter 14 reports Boltz-2 benchmarks that predate Boltz-2.1, which was released on 2025-06-11; the current release is 2.2.1. Chapter 15 says explicitly that something will have been released between writing and reading.

Chapters 13 and 15 were corrected before printing

AlphaFold 3 moved twice in 2026. Its code licence became Apache 2.0 in June, and its weights stopped being gated behind a request form in July. Both changes landed while this book was still in draft, so Chapters 13 and 15 were corrected to match before any reader saw them. No copy of the book states the older position, and neither change is an erratum.

The changelog below dates those two changes to when they happened upstream, not to when the chapters were edited. That is the date worth having. It tells you how old the situation a chapter describes actually is, which is what you need in order to judge whether a chapter written in 2026 still holds when you are reading it.

Changelog

What has moved upstream, newest first. The date is when the change happened, not when this page or a chapter was edited. Only changes to the software and its terms are recorded here; a correction to something the book itself got wrong belongs on the errata page.