Evidence map›Paper›PMID 42562988›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

In Silico Laboratory: New and Updated Tools for Protein-Centered Drug Discovery.

Dušanka Janežič, Janez Konc

Abstract read
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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.

Dušanka JanežičFaculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000, Koper, Slovenia.
Janez KoncFaculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000, Koper, Slovenia. konc@cmm.ki.si.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Computational tools for protein-ligand binding predictions are essential in modern drug discovery. This chapter provides an updated overview of the ProBiS tools, which identify binding sites, predict ligand interactions, and analyze conserved water molecules. Using an efficient maximum clique algorithm, these tools enable large-scale mining of protein structure databases, including the Protein Data Bank (PDB) and AlphaFoldDB, for drug repurposing and functional annotation. Recent advances include the ProBiS-Dock database, which provides precomputed binding sites for proteome-wide ligand-binding prediction, and the ProBiS-Dock algorithm, a hybrid flexible docking method. Additionally, ProBiS-H

Indexed as

Computational BiologyDrug DiscoveryProteinsAlgorithmsBinding SitesComputer SimulationDatabases, ProteinHumansLigandsMolecular Docking SimulationProtein BindingSoftwareLigandsProteinsAlphaFoldDBBinding site predictionConserved water moleculesDrug discoveryLigand dockingProBiS-Dock algorithmProBiS-Dock databaseProBiS-FoldProBiS-H2OProBiS-H2O MDProBiS toolsProtein–ligand binding

Identifiers

PMID42562988

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

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.