Michael Nilges

29 papers B 1Journal 27
YearRankTypeTitle / Venue / Authors
2024 J jnl
AlignScape, displaying sequence similarity using self-organizing maps.
Frontiers Bioinform.
Isaac Filella-Merce, Vincent Mallet, Eric Durand, Michael Nilges, Guillaume Bouvier, Riccardo Pellarin
2024 J jnl
Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets.
Bioinform.
Fabien Mareuil, Alexandra Moine-Franel, Anuradha Kar, Michael Nilges, Constantin Bogdan Ciambur, Olivier Sperandio
2022 J jnl
InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.
Bioinform.
Vincent Mallet, Luis Checa Ruano, Alexandra Moine-Franel, Michael Nilges, Karen Druart, Guillaume Bouvier, Olivier Sperandio
2021 J jnl
Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology.
PLoS Comput. Biol.
Hamed Khakzad, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran Van Nhieu, Johan Malmström, Lars Malmström
2021 J jnl
The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators.
Bioinform.
Rachel Torchet, Karen Druart, Luis Checa Ruano, Alexandra Moine-Franel, Hélène Borges, Olivia Doppelt-Azeroual, Bryan Brancotte, Fabien Mareuil, Michael Nilges, Hervé Ménager, Olivier Sperandio
2021 J jnl
quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories.
Bioinform.
Vincent Mallet, Michael Nilges, Guillaume Bouvier
2020 J jnl
ARIAweb: a server for automated NMR structure calculation.
Nucleic Acids Res.
Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux
2019 J jnl
Minimal NMR distance information for rigidity of protein graphs.
Discret. Appl. Math.
Carlile Lavor, Leo Liberti, Bruce Randall Donald, Bradley Worley, Benjamin Bardiaux, Thérèse E. Malliavin, Michael Nilges
2019 J jnl
mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics.
J. Chem. Inf. Model.
Damien Monet, Nathan Desdouits, Michael Nilges, Arnaud Blondel
2018 J jnl
Tuning interval Branch-and-Prune for protein structure determination.
J. Glob. Optim.
Bradley Worley, Florent Delhommel, Florence Cordier, Thérèse E. Malliavin, Benjamin Bardiaux, Nicolas Wolff, Michael Nilges, Carlile Lavor, Leo Liberti
2016 J jnl
Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa: d-Lac Ligase VanA.
J. Chem. Inf. Model.
Nathalie Duclert-Savatier, Guillaume Bouvier, Michael Nilges, Thérèse E. Malliavin
2016 J jnl
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.
Bioinform.
Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin
2016 J jnl
Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data.
PLoS Comput. Biol.
Simeon Carstens, Michael Nilges, Michael Habeck
2015 J jnl
An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.
BMC Bioinform.
Andrea Cassioli, Benjamin Bardiaux, Guillaume Bouvier, Antonio Mucherino, Rafael Alves, Leo Liberti, Michael Nilges, Carlile Lavor, Thérèse E. Malliavin
2015 J jnl
An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps.
Bioinform.
Guillaume Bouvier, Nathan Desdouits, Mathias Ferber, Arnaud Blondel, Michael Nilges
2015 J jnl
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis.
BMC Bioinform.
Emna Harigua-Souiai, Isidro Cortes-Ciriano, Nathan Desdouits, Thérèse E. Malliavin, Ikram Guizani, Michael Nilges, Arnaud Blondel, Guillaume Bouvier
2014 J jnl
Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps.
J. Chem. Inf. Model.
Guillaume Bouvier, Nathalie Duclert-Savatier, Nathan Desdouits, Djalal Meziane-Cherif, Arnaud Blondel, Patrice Courvalin, Michael Nilges, Thérèse E. Malliavin
2014 J jnl
ModBase, a database of annotated comparative protein structure models and associated resources.
Nucleic Acids Res.
Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali
2013 J jnl
A convective replica-exchange method for sampling new energy basins.
J. Comput. Chem.
Yannick G. Spill, Guillaume Bouvier, Michael Nilges
2013 — ch.
Distance Geometry in Structural Biology: New Perspectives.
Distance Geometry
Thérèse E. Malliavin, Antonio Mucherino, Michael Nilges
2013 J jnl
Erratum: A convective replica-exchange method for sampling new energy basins.
J. Comput. Chem.
Yannick G. Spill, Guillaume Bouvier, Michael Nilges
2011 J jnl
Grid computing for improving conformational sampling in NMR structure calculation.
Bioinform.
Fabien Mareuil, Christophe Blanchet, Therese E. Malliavin, Michael Nilges
2011 B conf
Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems.
SEA
Antonio Mucherino, Carlile Lavor, Therese E. Malliavin, Leo Liberti, Michael Nilges, Nelson Maculan
2010 J jnl
Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment.
J. Chem. Inf. Model.
David Giganti, Hélène Guillemain, Jean-Louis Spadoni, Michael Nilges, Jean-François Zagury, Matthieu Montès
2008 J jnl
ISD: a software package for Bayesian NMR structure calculation.
Bioinform.
Wolfgang Rieping, Michael Nilges, Michael Habeck
2008 J jnl
Structural Biology by NMR: Structure, Dynamics, and Interactions.
PLoS Comput. Biol.
Phineus R. Markwick, Therese E. Malliavin, Michael Nilges
2007 J jnl
ARIA2: Automated NOE assignment and data integration in NMR structure calculation.
Bioinform.
Wolfgang Rieping, Michael Habeck, Benjamin Bardiaux, Aymeric Bernard, Therese E. Malliavin, Michael Nilges
2007 J jnl
Biskit - A software platform for structural bioinformatics.
Bioinform.
Raik Grünberg, Michael Nilges, Johan Leckner
2003 J jnl
ARIA: automated NOE assignment and NMR structure calculation.
Bioinform.
Jens P. Linge, Michael Habeck, Wolfgang Rieping, Michael Nilges