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authFullName_s : Martin Zacharias

ATTRACT and PTOOLS: Open Source Programs for Protein–Protein Docking

Sebastian Schneider , Adrien Saladin , Sébastien Fiorucci , Chantal Prévost , Martin Zacharias et al.
Springer, New York, NY. Computational Drug Discovery and Design, 819, pp.221-232, 2012, Methods in Molecular Biology (Methods and Protocols), ⟨10.1007/978-1-61779-465-0_15⟩
Book sections hal-02545543v1

Exploiting Antigenic Diversity for Vaccine Design

Marco Soriani , Pierre Petit , Renata Grifantini , Roberto Petracca , Giovanni Gancitano et al.
Journal of Biological Chemistry, 2010, 285 (39), pp.30126-30138. ⟨10.1074/jbc.M110.118513⟩
Journal articles hal-02545563v1

Electrostatic profiles of targets NMB0033 and CT043

Sébastien Fiorucci , Martin Zacharias
BacAbs meeting, Mar 2008, Milan, Italy
Conference papers hal-02546318v1
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Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.

Adrien Saladin , Christopher Amourda , Pierre Poulain , Nicolas Férey , Marc Baaden et al.
Nucleic Acids Research, 2010, 38 (19), pp.6313-23. ⟨10.1093/nar/gkq459⟩
Journal articles hal-00533099v1

A folding switch regulates interleukin 27 biogenesis and secretion of its α-subunit as a cytokine

Stephanie Müller , Antonie Friedl , Isabel Aschenbrenner , Julia Esser-von Bieren , Martin Zacharias et al.
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (5), pp.1585-1590. ⟨10.1073/pnas.1816698116⟩
Journal articles hal-03994426v1

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.

Sarel J Fleishman , Timothy A Whitehead , Eva-Maria Strauch , Jacob E Corn , Sanbo Qin et al.
Journal of Molecular Biology, 2011, 414 (2), in press. ⟨10.1016/j.jmb.2011.09.031⟩
Journal articles inria-00637848v1
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Altered fibrin clot structure and dysregulated fibrinolysis contribute to thrombosis risk in severe COVID-19

Malgorzata Wygrecka , Anna Birnhuber , Benjamin Seeliger , Laura Michalick , Oleg Pak et al.
Blood Advances, 2022, 6 (3), pp.1074-1087. ⟨10.1182/bloodadvances.2021004816⟩
Journal articles hal-03873011v1

Update of the ATTRACT force field for the prediction of protein-protein binding affinity

Jean-Baptiste Chéron , Martin Zacharias , Serge Antonczak , Sébastien Fiorucci
Journal of Computational Chemistry, 2017, 38 (21), pp.1887-1890. ⟨10.1002/jcc.24836⟩
Journal articles hal-02545204v1

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Rocco Moretti , Sarel J Fleishman , Rudi Agius , Mieczyslaw Torchala , Paul A. Bates et al.
Proteins - Structure, Function and Bioinformatics, 2013, 81 (11), pp.1980 - 1987. ⟨10.1002/prot.24356⟩
Journal articles hal-00905794v1

Antigen/Antibody docking improvement including hotspot and solvation energy

Sébastien Fiorucci , Martin Zacharias
BacAbs meeting, Jan 2008, Barcelone, Spain
Conference papers hal-02546320v1

Altered fibrin clot structure contributes to thrombosis risk in severe COVID-19

Malgorzata Wygrecka , Anna Birnhuber , Benjamin Seeliger , Laura Michalick , Oleg Pak et al.
Preprints, Working Papers, ... hal-03438497v1
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An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA

Benjamin Boyer , Johann Ezelin , Pierre Poulain , Adrien Saladin , Martin Zacharias et al.
PLoS ONE, 2015, 10 (3), pp.e0116414. ⟨10.1371/journal.pone.0116414⟩
Journal articles hal-01230983v1
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PTools: an opensource molecular docking library.

Adrien Saladin , Sébastien Fiorucci , Pierre Poulain , Chantal Prévost , Martin Zacharias et al.
BMC Structural Biology, 2009, 9, pp.27. ⟨10.1186/1472-6807-9-27⟩
Journal articles inserm-00474185v1
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Modeling large protein–glycosaminoglycan complexes using a fragment‐based approach

Sergey Samsonov , Martin Zacharias , Isaure Chauvot de Beauchêne
Journal of Computational Chemistry, 2019, 40 (14), pp.1429-1439. ⟨10.1002/jcc.25797⟩
Journal articles hal-02088192v1

Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT

Sébastien Fiorucci , Martin Zacharias
Proteins - Structure, Function and Bioinformatics, 2010, 78 (15), pp.3131-3139. ⟨10.1002/prot.22808⟩
Journal articles istex hal-02545568v1
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Fragment­ based modeling of protein­-GAG complexes

Isaure Chauvot de Beauchêne , Sergey A Samsonov , Martin Zacharias
GGMM 2017 - 20e congrès du Groupe de Graphisme et Modelisation Moleculaire, May 2017, Reims, France. pp.1
Conference poster hal-01927283v1
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Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Christina Eva Maria Schindler , Isaure Chauvot de Beauchêne , Sjoerd Jacob de Vries , Martin Zacharias
Proteins: Structure, Function, and Genetics, 2017, ⟨10.1002/prot.25196⟩
Journal articles hal-01505867v1

Prediction of Protein-Protein Interaction Sites Using Electrostatic Desolvation Profiles

Sébastien Fiorucci , Martin Zacharias
Biophysical Journal, 2010, 98 (9), pp.1921-1930. ⟨10.1016/j.bpj.2009.12.4332⟩
Journal articles hal-02545575v1

Blind prediction of interfacial water positions in CAPRI

Marc F. Lensink , Aiain H. Moal , Paul A. Bates , Panagiotis L. Kastritis , Adrien S. J. Melquiond et al.
Proteins - Structure, Function and Bioinformatics, 2014, 82 (4), pp.620-632. ⟨10.1002/prot.24439⟩
Journal articles hal-00880345v1

Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach

Glenn Glashagen , Sjoerd de Vries , Urszula Uciechowska-Kaczmarzyk , Sergey A. Samsonov , Samuel Murail et al.
Proteins - Structure, Function and Bioinformatics, 2019, 88 (8), pp.1018-1028. ⟨10.1002/prot.25860⟩
Journal articles hal-03201555v1
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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking

Alexander Sasse , Sjoerd Jacob de Vries , Christina Eva Maria Schindler , Isaure Chauvot de Beauchêne , Martin Zacharias et al.
Journal articles hal-01505866v1
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Fragment-based modeling of protein-bound ssRNA

Isaure Chauvot de Beauchêne , Sjoerd J de Vries , Martin Zacharias
ECCB 2016: The 15th European Conference on Computational Biology, Sep 2016, Den Haag, Netherlands. 2016
Conference poster hal-01573352v1

Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces

Sébastien Fiorucci , Martin Zacharias
Immunoinformatics, pp.365-374, 2014, ⟨10.1007/978-1-4939-1115-8_20⟩
Book sections hal-02545222v1