Evidence map›Paper›PMID 38965117›Full record

ReviewTopics in current chemistry (Cham)2024

The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.

Saber Saharkhiz, Mehrnaz Mostafavi, Amin Birashk, Shiva Karimian, Shayan Khalilollah, Sohrab Jaferian, Yalda Yazdani, Iraj Alipourfard, Yun Suk Huh, Marzieh Ramezani Farani and 1 more

Abstract readReview
In one paragraph

Review in Topics in current chemistry (Cham), 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
–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

2 citing papers in PubMed.

  1. Review
  2. 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

11 authors.

Saber SaharkhizDivision of Neuroscience, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
Mehrnaz MostafaviFaculty of Allied Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
Amin BirashkDepartment of Computer Science, The University of Texas at Dallas, Richardson, TX, USA.
Shiva KarimianElectrical and Computer Research Center, Sanandaj Azad University, Sanandaj, Iran.
Shayan KhalilollahDepartment of Neurosurgery, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
Sohrab JaferianGoergen Institute for Data Science, University of Rochester, Rochester, NY, USA.
Yalda YazdaniImmunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. yaldayznn@gmail.com.
Iraj AlipourfardInstitute of Physical Chemistry, Polish Academy of Sciences, Marcina Kasprzaka 44/52, 01-224, Warsaw, Poland. ialipourfard@ichf.edu.pl.
Yun Suk HuhDepartment of Biological Engineering, Inha University, Incheon, Republic of Korea.
Marzieh Ramezani FaraniDepartment of Biological Engineering, Inha University, Incheon, Republic of Korea.
Reza Akhavan-SigariDepartment of Neurosurgery, University Medical Center, Tuebingen, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In recent years, there has been a notable increase in the scientific community's interest in rational protein design. The prospect of designing an amino acid sequence that can reliably fold into a desired three-dimensional structure and exhibit the intended function is captivating. However, a major challenge in this endeavor lies in accurately predicting the resulting protein structure. The exponential growth of protein databases has fueled the advancement of the field, while newly developed algorithms have pushed the boundaries of what was previously achievable in structure prediction. In particular, using deep learning methods instead of brute force approaches has emerged as a faster and more accurate strategy. These deep-learning techniques leverage the vast amount of data available in protein databases to extract meaningful patterns and predict protein structures with improved precision. In this article, we explore the recent developments in the field of protein structure prediction. We delve into the newly developed methods that leverage deep learning approaches, highlighting their significance and potential for advancing our understanding of protein design.

Indexed as

Deep LearningProtein ConformationProteinsAlgorithmsDatabases, ProteinProteinsDeep learningProtein engineeringProtein structure predictionRational design

Identifiers

PMID38965117
PMCPMC11224075

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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.