Evidence map›Paper›PMID 23280336›Full record

ArticleMethods (San Diego, Calif.)2013

Generating conformation-specific synthetic antibodies to trap proteins in selected functional states.

Marcin Paduch, Akiko Koide, Serdar Uysal, Shahir S Rizk, Shohei Koide, Anthony A Kossiakoff

Open access · greenAbstract read
In one paragraph

Article in Methods (San Diego, Calif.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.

0numbers the graph read from it
0cells of the map it votes in
72citing papers in PubMed
6.5field-weighted citation impact, top 3% 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

72 citing papers in PubMed, 109 citations in OpenAlex.

  1. Article
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  4. Review
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  9. Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution.Proceedings of the National Academy of Sciences of the United States of America · 2025
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  14. Chaperone-assisted cryo-EM structure ofbioRxiv : the preprint server for biology · 2024
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  19. Structure of saguaro cactus virus 3' translational enhancer mimics 5' cap for eIF4E binding.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  20. Article

12 more citing papers are in PubMed but not listed here.

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 at 1 institution in 1 country.

Marcin PaduchDepartment of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
Akiko Koide
Serdar Uysal
Shahir S Rizk
Shohei Koide
Anthony A Kossiakoff
University of Chicago · US

Funding

Synthetic Antigen Binder CoreU54GM087519 · NIGMS · UNIVERSITY OF CHICAGO · PI NAKAMOTO, ROBERT K. · 2010 to 2017
$31.9M
Subproject 5U54GM074946 · NIGMS · UNIVERSITY OF CALIF-LOS ALAMOS NAT LAB · PI TERWILLIGER, THOMAS C. · 2005 to 2009
$20.2M
Recombinant Antibody NetworkU54HG006436 · NHGRI · UNIVERSITY OF CHICAGO · PI KOSSIAKOFF, ANTHONY A · 2011 to 2014
$8.2M
Foreign - Univ. of Toronto, PI-Dr. Sachdev SidhuU01GM094588 · NIGMS · UNIVERSITY OF CHICAGO · PI KOSSIAKOFF, ANTHONY A · 2010 to 2014
$6.8M
Chaperone Assisted CrystallographyR01GM072688 · NIGMS · UNIVERSITY OF CHICAGO · PI KOSSIAKOFF, ANTHONY A · 2005 to 2012
$2.7M
NHGRI NIH HHS U54 HG006436NHGRI NIH HHS U54-HG006436NIGMS NIH HHS R01 GM072688NIGMS NIH HHS R01-GM072688NIGMS NIH HHS U01 GM094588NIGMS NIH HHS U01-GM094588NIGMS NIH HHS U54 GM074946NIGMS NIH HHS U54 GM087519NIGMS NIH HHS U54-GM087519
6 · The paper itself

Abstract

A set of phage display sorting strategies and validation methodologies are presented that are capable of producing high performance synthetic antibodies (sABs) with customized properties. Exquisite control of antigen and conditions during the phage display selection process can yield sABs that: (1) recognize conformational states, (2) target specific regions of the surface of a protein, (3) induce conformational changes, and (4) capture and stabilize multi-protein complexes. These unique capabilities open myriad opportunities to study complex macromolecular processes inaccessible to traditional affinity reagent technology. We present detailed protocols for de novo isolation of binders, as well as examples of downstream biophysical characterization. The methods described are generalizable and can be adapted to other in vitro direct evolution approaches based on yeast or mRNA display.

Indexed as

Antibody SpecificityAntibodiesEnzyme-Linked Immunosorbent AssayMolecular ConformationPeptide LibraryProteinsAntibodiesPeptide LibraryProteins

Identifiers

PMID23280336
PMCPMC3650108
OpenAlexW1979900371

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.