Evidence map›Paper›PMID 37676602›Full record

ReviewMethods in molecular biology (Clifton, N.J.)2024

Recent Deep Learning Applications to Structure-Based Drug Design.

Jacob Verburgt, Anika Jain, Daisuke Kihara

Open access · greenAbstract readReview
In one paragraph

Review in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
3.0field-weighted citation impact, top 9% of its field
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

2 citing papers in PubMed, 3 citations in OpenAlex.

  1. Review
  2. Article
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

3 authors at 1 institution in 1 country.

Jacob VerburgtDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Anika JainDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Daisuke KiharaDepartment of Biological Sciences, Purdue University, West Lafayette, IN, USA. dkihara@purdue.edu.
Purdue University West Lafayette · US

Funding

Purdue University Molecular Biophysics Training ProgramT32GM132024 · NIGMS · PURDUE UNIVERSITY · PI Angeline Marie Lyon, John Tesmer · 2019 to 2026
$2.0M
Building protein structure models for intermediate resolution cryo-electron microscopy mapsR01GM133840 · NIGMS · PURDUE UNIVERSITY · PI KIHARA, DAISUKE · 2020 to 2023
$1.6M
NIGMS NIH HHS R01 GM133840NIGMS NIH HHS T32 GM132024
6 · The paper itself

Abstract

Identification and optimization of small molecules that bind to and modulate protein function is a crucial step in the early stages of drug development. For decades, this process has benefitted greatly from the use of computational models that can provide insights into molecular binding affinity and optimization. Over the past several years, various types of deep learning models have shown great potential in improving and enhancing the performance of traditional computational methods. In this chapter, we provide an overview of recent deep learning-based developments with applications in drug discovery. We classify these methods into four subcategories dependent on the task each method is aiming to solve. For each subcategory, we provide the general framework of the approach and discuss individual methods.

Indexed as

Deep LearningDrug DesignDrug DevelopmentDrug DiscoveryAb initio molecule generationComputational molecule representationComputer-aided drug designDeep learningGenerative-adversarial networks (GANs)Lead optimizationLigand pose generationLigand pose scoringPharmacokinetic optimizationStructure-based drug design

Identifiers

PMID37676602
PMCPMC10578466
OpenAlexW4386497647

What OpenQuestion holds

Textmetadata
LicenceTDM
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.