Evidence map›Paper›PMID 39976676›Full record

ArticleHuman genetics2025

Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges.

Paola Turina, Maria Petrosino, Carlos A Enriquez Sandoval, Leonore Novak, Alessandra Pasquo, Emil Alexov, Muttaqi Ahmad Alladin, David B Ascher, Giulia Babbi, Constantina Bakolitsa and 29 more

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In one paragraph

Article in Human genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

39 authors.

Paola Turina *Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Maria Petrosino *Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Roma, 00185, Rome, Italy.
Carlos A Enriquez SandovalDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Leonore NovakDepartment of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Roma, 00185, Rome, Italy.
Alessandra PasquoDiagnostics and Metrology Laboratory FSN-TECFIS-DIM, ENEA CR Frascati, 00044, Frascati, Italy.
Emil AlexovDepartment of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
Muttaqi Ahmad AlladinDepartment of Computational and Data Sciences, Indian Institute of Science, Bangaluru, 560012, India.
David B AscherComputational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
Giulia BabbiDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Constantina BakolitsaDepartment of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
Rita CasadioDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Jianlin ChengDepartment of Electrical Engineering and Computer Science, NextGen Precision Health Institute, University of Missouri, Columbia, MO, 65211, USA.
Piero FariselliDepartment of Medical Sciences, University of Torino, 10126, Torino, Italy.
Lukas FolkmanInstitute for Integrated and Intelligent Systems, Griffith University, Southport, QLD, 4222, Australia.
Akash KamandulaKhoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA.
Panagiotis KatsonisDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Minghui LiSchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, China.
Dong LiComputational Biology and Bioinformatics, Université Libre de Bruxelles, 1050, Brussels, Belgium.
Olivier LichtargeDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Sajid MahmudDepartment of Electrical Engineering and Computer Science, NextGen Precision Health Institute, University of Missouri, Columbia, MO, 65211, USA.
Pier Luigi MartelliDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Debnath PalDepartment of Computational and Data Sciences, Indian Institute of Science, Bangaluru, 560012, India.
Shailesh Kumar PandayDepartment of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
Douglas E V PiresSchool of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, 3053, Australia.
Stephanie PortelliComputational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
Fabrizio PucciComputational Biology and Bioinformatics, Université Libre de Bruxelles, 1050, Brussels, Belgium.
Carlos H M RodriguesComputational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
Marianne RoomanComputational Biology and Bioinformatics, Université Libre de Bruxelles, 1050, Brussels, Belgium.
Castrense SavojardoDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy.
Martin SchwersenskyComputational Biology and Bioinformatics, Université Libre de Bruxelles, 1050, Brussels, Belgium.
Yang ShenDepartment of Electrical and Computer Engineering Texas, A&M University, College Station, TX, 77843, USA.
Alexey V StrokachDepartment of Computer Science, University of Toronto, Toronto, ON, M5S 2E4, Canada.
Yuanfei SunDepartment of Electrical and Computer Engineering Texas, A&M University, College Station, TX, 77843, USA.
Junwoo Woo3 Billion, Seoul, South Korea.
Predrag RadivojacKhoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA.
Steven E BrennerDepartment of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
Roberta ChiaraluceDepartment of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Roma, 00185, Rome, Italy. roberta.chiaraluce@uniroma1.it.
Valerio ConsalviDepartment of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Roma, 00185, Rome, Italy. valerio.consalvi@uniroma1.it.
Emidio CapriottiDepartment of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy. emidio.capriotti@unibo.it.

Funding

Cognitive Computing of Alzheimer's Disease Genes and RiskU01AG068214 · NIA · BAYLOR COLLEGE OF MEDICINE · PI LICHTARGE, OLIVIER · 2021 to 2025
$4.4M
New Generation DelPhi: large systems and beyond electrostaticsR01GM093937 · NIGMS · CLEMSON UNIVERSITY · PI ALEXOV, EMIL GEORGIEV · 2010 to 2023
$4.3M
Integrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8M
Center for Critical Assessment of Genome InterpretationU24HG007346 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI BRENNER, STEVEN E, IOANNIDIS, NILAH MONNIER · 2020 to 2025
$3.8M
Unraveling molecular and system-level mechanisms of human disease-associated protein mutationsR35GM124952 · NIGMS · TEXAS ENGINEERING EXPERIMENT STATION · PI Yang Shen · 2017 to 2026
$2.9M
Component 2 - Resource ProjectU41HG007346 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI BRENNER, STEVEN E · 2015 to 2017
$1.7M
DelPhi and associated resources: maintenance, development and applicationsR35GM151964 · NIGMS · CLEMSON UNIVERSITY · PI Emil Georgiev Alexov · 2024 to 2026
$1.1M
Critical Assessment of Genome Interpretation ConferenceR13HG006650 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI BRENNER, STEVEN E · 2011 to 2018
$165k
Australian National Health and Medical Research Council GNT1174405Ministero dell'Istruzione, dell'Università e della Ricerca ELIXIRNextGenIT Grant Code IR0000010Ministero dell'Istruzione, dell'Università e della Ricerca MIUR-PRIN-201744NR8SNational Institute of General Medical Sciences, United States R01GM093123National Institute of General Medical Sciences, United States R35GM124952National Institute of Health, United States AG068214National Institute of Health, United States R01GM093937National Institute of Heath, United States R35GM151964National Natural Science Foundation of China 32070665National Science Foundation, United States DBI2308699NHGRI NIH HHS R13 HG006650NHGRI NIH HHS U24 HG007346NHGRI NIH HHS U41 HG007346NIA NIH HHS U01 AG068214NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM093937NIGMS NIH HHS R35 GM124952NIGMS NIH HHS R35 GM151964
6 · The paper itself

Abstract

New thermodynamic and functional studies have been recently conducted to evaluate the impact of amino acid substitutions on the Mitogen Activated Protein Kinases 1 and 3 (MAPK1/3). The Critical Assessment of Genome Interpretation (CAGI) data provider, at Sapienza University of Rome, measured the unfolding free energy and the enzymatic activity of a set of variants (MAPK challenge dataset). Thermodynamic measurements for the denaturant-induced equilibrium unfolding of the phosphorylated and unphosphorylated forms of the MAPKs were obtained by monitoring the far-UV circular dichroism and intrinsic fluorescence changes as a function of denaturant concentration. These values have been used to calculate the change in unfolding free energy between the variant and wild-type proteins at zero concentration of denaturant (

Indexed as

Amino Acid SubstitutionMitogen-Activated Protein Kinase 1Mitogen-Activated Protein Kinase 3Circular DichroismHumansPhosphorylationThermodynamicsMitogen-Activated Protein Kinase 1Mitogen-Activated Protein Kinase 3

Identifiers

PMID39976676
PMCPMC11975483

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