Evidence map›Paper›PMID 36098536›Full record

ArticleJournal of chemical information and modeling2022

On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction.

Jannis Born, Yoel Shoshan, Tien Huynh, Wendy D Cornell, Eric J Martin, Matteo Manica

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

6 authors.

Jannis BornAccelerated Discovery, IBM Research Europe, 8803 Rüschlikon, Switzerland.ORCID 0000-0001-8307-5670
Yoel ShoshanIBM Research Haifa, Q288+48 Haifa 31905, Israel.
Tien HuynhIBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.
Wendy D CornellIBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States.
Eric J MartinNovartis Institutes for BioMedical Research, Emeryville, California 94608, United States.ORCID 0000-0001-7040-5108
Matteo ManicaAccelerated Discovery, IBM Research Europe, 8803 Rüschlikon, Switzerland.ORCID 0000-0002-8872-0269

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent work showed that active site rather than full-protein-sequence information improves predictive performance in kinase-ligand binding affinity prediction. To refine the notion of an "active site", we here propose and compare multiple definitions. We report significant evidence that our novel definition is superior to previous definitions and better models of ATP-noncompetitive inhibitors. Moreover, we leverage the discontiguity of the active site sequence to motivate novel protein-sequence augmentation strategies and find that combining them further improves performance.

Indexed as

Adenosine TriphosphateAmino Acid SequenceBinding SitesLigandsProtein BindingAdenosine TriphosphateLigands

Identifiers

PMID36098536
PMCPMC9516689

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.