Evidence map›Paper›PMID 34228913›Full record

ArticleACS chemical biology2021

Identification of Secondary Binding Sites on Protein Surfaces for Rational Elaboration of Synthetic Protein Mimics.

Justin M Torner, Yuwei Yang, David Rooklin, Yingkai Zhang, Paramjit S Arora

Abstract read
In one paragraph

Article in ACS chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Reengineering of a Proteomimetic Pan-Ras Inhibitor into a Ras Degrader.Angewandte Chemie (International ed. in English) · 2025
    Article
  2. Article
  3. Article
  4. Article
  5. Integrated Molecular Modeling and Machine Learning for Drug Design.Journal of chemical theory and computation · 2023
    Review
  6. Article
  7. 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

5 authors.

Justin M TornerDepartment of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States.
Yuwei YangDepartment of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States.
David RooklinDepartment of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States.
Yingkai ZhangDepartment of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States.ORCID 0000-0002-4984-3354
Paramjit S AroraDepartment of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States.ORCID 0000-0001-5315-401X

Funding

Protein Domain Mimics as Modulators of Biomolecular InteractionsR35GM130333 · NIGMS · NEW YORK UNIVERSITY · PI Paramjit S Arora · 2019 to 2026
$6.0M
Computational modulator design and machine learning to target protein-protein interactionsR35GM127040 · NIGMS · NEW YORK UNIVERSITY · PI Yingkai Zhang · 2018 to 2026
$4.6M
Computational inhibitor design to target protein-protein interactionsR01GM120736 · NIGMS · NEW YORK UNIVERSITY · PI ARORA, PARAMJIT S, ZHANG, YINGKAI · 2016 to 2019
$1.6M
NIGMS NIH HHS R01 GM120736NIGMS NIH HHS R35 GM127040NIGMS NIH HHS R35 GM130333
6 · The paper itself

Abstract

Minimal mimics of protein conformations provide rationally designed ligands to modulate protein function. The advantage of minimal mimics is that they can be chemically synthesized and coaxed to be proteolytically resistant; a key disadvantage is that minimization of the protein binding epitope may be associated with loss of affinity and specificity. Several approaches to overcome this challenge may be envisioned, including deployment of covalent warheads and use of nonnatural residues to improve contacts with the binding surface. Herein, we describe our computational and experimental efforts to enhance the minimal protein mimics with fragments that can contact undiscovered binding pockets on Mdm2 and MdmX-two well-studied protein partners of p53.

Indexed as

Binding SitesCell Cycle ProteinsHumansLigandsMolecular Docking SimulationPeptidesProtein BindingProtein Conformation, alpha-HelicalProto-Oncogene ProteinsProto-Oncogene Proteins c-mdm2Cell Cycle ProteinsLigandsMDM2 protein, humanMDM4 protein, humanPeptidesProto-Oncogene ProteinsProto-Oncogene Proteins c-mdm2

Identifiers

PMID34228913
PMCPMC8344045

What OpenQuestion holds

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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.