MM/PBSA (AMBER)
End-state free energy method that scores the final frame of a short restrained-then-free molecular dynamics simulation with molecular mechanics and Poisson-Boltzmann surface area terms.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. One linked record has results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- MM/PBSA scoring after a 1 ns simulation Configuration · configuration · 1 evaluation · 10 results
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Use this method
How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Original source · bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344)
Technical metadata and extraction receipts
Stable ID: uc-leadopt-20261022-method-mmpbsa
- areas
- molecular-interactions
- contexts
- research
- method types
- conventional_pipeline
- entity level
- method
- reported name
- MM/PBSA
- access
- AMBER implementation.
- source locator
- Appendix D.2.2, 'Baselines'
- missing metadata
- version: reason: unreported; note: The supplement cites the AMBER implementation but prints no version
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; ai-assisted-source-review; method note: Re-retrieved all three sources and matched each pinned SHA-256. Re-rendered the Boltz-2 supplement with pdftotext -layout (poppler 26.08.0) and matched the text layer's recorded SHA-256. Re-read all 256 cells with a parser written for this review that does not import the extraction script, matching each result to its cell through its own source_locator, and separately read appendix tables 11, 12 and 14 from PNG renderings of PDF pages 29 and 30 at 160 dpi, and Ross Table 3 from the pinned XML markup. Checked printed value, numeric value, locator, metric concept, qualifier, direction, unit, uncertainty and the linked configuration, protocol and dataset, and that every N/A or '-' cell is recorded as missing with a reason.; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; reviewed at: 2026-10-22T13:40:00Z; artifact sha256: be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/supplementaryFiles
Related records
- configuration of: MM/PBSA scoring after a 1 ns simulation