Visualization of Properties in the Fragment Molecular Orbital Method Using Facio.

Masahiko Suenaga, Dmitri G Fedorov

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Masahiko SuenagaDepartment of Advanced Materials Science and Engineering, Faculty of Engineering Sciences, Kyushu University, 6-1, Kasugakoen, Kasuga City, Fukuoka, 816-8580, Japan.

Dmitri G FedorovMaterials DX Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan. d.g.fedorov@aist.go.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

For evaluating binding in biochemical systems, the fragment molecular orbital method is used to calculate interaction and binding energies at various levels of theory. The graphical user interface program Facio is used to prepare input files and visualize fragment properties, supporting rational design of new molecular agents. The protein-ligand binding in the complex of HIV protease 6X mutant with an AB-2 ligand (PDB: 2HC0) is studied with various analyses.

Indexed as

HIV ProteaseSoftwareDrug DesignLigandsModels, MolecularProtein BindingHIV ProteaseLigandsDFTB3FacioFluctuation analysisFMOFragment molecular orbital methodGAMESSHIV proteaseHotspot analysisMP2Pair interaction energyPartition analysisPIEDAProtein–ligand bindingRational drug designSubsystem analysisVisualization

Identifiers

PMID42604894

DOI10.1021/acs.jpclett.2c00040

What OpenQuestion holds

Textmetadata

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.