AlphaFold2 for protein structure prediction: Best practices and critical analyses

Authors: Radjasandirane, Ragousandirane, de Brevern, Alexandre G.

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2403.12668

Insights for variant clinical interpretation based on a benchmark of 65 variant effect predictors

Authors: Radjasandirane, Ragousandirane, Diharce, Julien, Gelly, Jean-Christophe ¹, de Brevern, Alexandre G. ^{⁎, 1}

Source: In Genomics May 2025 117(3)

Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".

Authors: de Brevern, Alexandre G.^1,2 (AUTHOR) alexandre.debrevern@univ-paris-diderot.fr

Source: International Journal of Molecular Sciences. Oct2024, Vol. 25 Issue 19, p10793. 13p.

Subject Terms: *ALLOSTERIC proteins, *PROTEIN kinase C, *SECOND messengers (Biochemistry), *PROTEIN domains, *CYTOSKELETAL proteins, *ALLOSTERIC regulation

An agnostic analysis of the human AlphaFold2 proteome using local protein conformations

Authors: de Brevern, Alexandre G.

Source: Biochimie. 207:11-19

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100188046216.0x000001&indx=1&recIds=ETOCvdc_100188046216.0x000001

Prediction of structural alphabet protein blocks using data mining

Authors: Maljković, Mirjana M., Mitić, Nenad S., de Brevern, Alexandre G.

Source: In Biochimie June 2022 197:74-85

Shaking the β-Bulges

Authors: Craveur, Pierrick, Narwani, Tarun J., Srinivasan, Narayanaswamy, Gelly, Jean-Christophe, Rebehmed, Joseph, de Brevern, Alexandre G.

Source: IEEE/ACM transactions on computational biology and bioinformatics. 19(1):14-18

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139892858.0x000001&indx=1&recIds=ETOCvdc_100139892858.0x000001

CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia

Authors: El Jahrani, Nora, Cretin, Gabriel, de Brevern, Alexandre G.

Source: Platelets. 33(1):157-167

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100139341681.0x000001&indx=1&recIds=ETOCvdc_100139341681.0x000001

Transient association between proteins elicits alteration of dynamics at sites far away from interfaces

Authors: Tandon, Himani, de Brevern, Alexandre G., Srinivasan, Narayanaswamy

Source: In Structure 1 April 2021 29(4):371-384

A Review of the Literature Organized Into a New Database: RHeference

Authors: Floch, Aline, Téletchéa, Stéphane, Tournamille, Christophe, de Brevern, Alexandre G., Pirenne, France

Source: In Transfusion Medicine Reviews April 2021 35(2):70-77

Impact of protein dynamics on secondary structure prediction

Authors: de Brevern, Alexandre G.

Source: In Biochimie December 2020 179:14-22

A structural entropy index to analyse local conformations in intrinsically disordered proteins

Authors: Akhila, Melarkode Vattekatte, Narwani, Tarun Jairaj, Floch, Aline, Maljković, Mirjana, Bisoo, Soubika, Shinada, Nicolas K., Kranjc, Agata, Gelly, Jean-Christophe, Srinivasan, Narayanaswamy, Mitić, Nenad, de Brevern, Alexandre G.

Source: In Journal of Structural Biology 1 April 2020 210(1)

A perspective on the sharing of docking data

Authors: Aci-Sèche, Samia, Bourg, Stéphane, Bonnet, Pascal, Rebehmed, Joseph, de Brevern, Alexandre G., Diharce, Julien

Source: Data in brief. 49

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195354592.0x000001&indx=1&recIds=ETOCvdc_100195354592.0x000001

Structural variations within proteins can be as large as variations observed across their homologues

Authors: Vetrivel, Iyanar, de Brevern, Alexandre G., Cadet, Frédéric, Srinivasan, Narayanaswamy, Offmann, Bernard

Source: In Biochimie December 2019 167:162-170

Dimerization and phosphorylation of Lutheran/basal cell adhesion molecule are critical for its function in cell migration on laminin

Alternate Title: Lu dimerization and phosphorylation mediate cell migration (English)

Authors: Guadall, Anna, Cochet, Sylvie, Renaud, Olivier ^**, Colin, Yves, Le Van Kim, Caroline, de Brevern, Alexandre G., El Nemer, Wassim

Source: In Journal of Biological Chemistry 11 October 2019 294(41):14911-14921

In silico prediction of protein flexibility with local structure approach

Authors: Narwani, Tarun J., Etchebest, Catherine, Craveur, Pierrick, Léonard, Sylvain, Rebehmed, Joseph, Srinivasan, Narayanaswamy, Bornot, Aurélie, Gelly, Jean-Christophe, de Brevern, Alexandre G.

Source: In Biochimie October 2019 165:150-155

Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia.

Authors: Radjasandirane, Ragousandirane¹ (AUTHOR), de Brevern, Alexandre G.¹ (AUTHOR) alexandre.debrevern@univ-paris-diderot.fr

Source: Biomolecules (2218-273X). Mar2023, Vol. 13 Issue 3, p509. 25p.

Subject Terms: *MOLECULAR dynamics, *THROMBOCYTOSIS, *CALRETICULIN, *STRUCTURAL models

Discrete analyses of protein dynamics

Authors: Narwani, Tarun Jairaj, Craveur, Pierrick, Shinada, Nicolas K., Floch, Aline, Santuz, Hubert, Vattekatte, Akhila Melarkode, Srinivasan, Narayanaswamy, Rebehmed, Joseph, Gelly, Jean-Christophe, Etchebest, Catherine, de Brevern, Alexandre G.

Source: Journal of biomolecular structure & dynamics. 38(10):2988-3002

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100111262097.0x000001&indx=1&recIds=ETOCvdc_100111262097.0x000001

A Simple Analysis of the Second (Extra) Disulfide Bridge of V H Hs.

Authors: Martins, Carla, Gardebien, Fabrice, Nadaradjane, Aravindan Arun, Diharce, Julien, de Brevern, Alexandre G.

Source: Molecules; Oct2024, Vol. 29 Issue 20, p4863, 13p

Subject Terms: CONFORMATIONAL analysis, MOLECULAR dynamics, PROTEIN conformation, BIOTECHNOLOGY, IMMUNOGLOBULINS

Should We Expect a Second Wave of AlphaFold Misuse After the Nobel Prize?

Authors: de Brevern, Alexandre G.¹ (AUTHOR) alexandre.debrevern@univ-paris-diderot.fr

Source: BioMedInformatics. Dec2024, Vol. 4 Issue 4, p2306-2308. 3p.

Subject Terms: *ALTERNATIVE RNA splicing, *STRUCTURAL models, *MEMBRANE proteins, *PROTEIN conformation, *PROTEIN structure, *PROTEIN folding

A Perspective on the (Rise and Fall of) Protein β-Turns.

Authors: de Brevern, Alexandre G.¹ (AUTHOR) alexandre.debrevern@univ-paris-diderot.fr

Source: International Journal of Molecular Sciences. Oct2022, Vol. 23 Issue 20, p12314-N.PAG. 14p.

Subject Terms: *PROTEIN conformation, *PROTEIN structure, *HYDROGEN bonding, *PROTEINS, *LOCAL knowledge