ARIA: automated NOE assignment and NMR structure calculation. - Jens P. Linge; Michael Habeck; Wolfgang Rieping; Michael Nilges (Bioinform., 2003)

Biskit - A software platform for structural bioinformatics. - Raik Grünberg; Michael Nilges; Johan Leckner (Bioinform., 2007)

ARIA2: Automated NOE assignment and data integration in NMR structure calculation. - Wolfgang Rieping; Michael Habeck; Benjamin Bardiaux; Aymeric Bernard; Therese E. Malliavin; Michael Nilges (Bioinform., 2007)

ISD: a software package for Bayesian NMR structure calculation. - Wolfgang Rieping; Michael Nilges; Michael Habeck (Bioinform., 2008)

Structural Biology by NMR: Structure, Dynamics, and Interactions. - Phineus R. Markwick; Therese E. Malliavin; Michael Nilges (PLoS Comput. Biol., 2008)

Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment. - David Giganti; Hélène Guillemain; Jean-Louis Spadoni; Michael Nilges; Jean-François Zagury; Matthieu Montès (J. Chem. Inf. Model., 2010)

Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems. - Antonio Mucherino; Carlile Lavor; Therese E. Malliavin; Leo Liberti; Michael Nilges; Nelson Maculan (SEA, 2011)

Grid computing for improving conformational sampling in NMR structure calculation. - Fabien Mareuil; Christophe Blanchet; Therese E. Malliavin; Michael Nilges (Bioinform., 2011)

Distance Geometry in Structural Biology: New Perspectives. - Thérèse E. Malliavin; Antonio Mucherino; Michael Nilges (Distance Geometry, 2013)

A convective replica-exchange method for sampling new energy basins. - Yannick G. Spill; Guillaume Bouvier; Michael Nilges (J. Comput. Chem., 2013)

Erratum: A convective replica-exchange method for sampling new energy basins. - Yannick G. Spill; Guillaume Bouvier; Michael Nilges (J. Comput. Chem., 2013)

Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps. - Guillaume Bouvier; Nathalie Duclert-Savatier; Nathan Desdouits; Djalal Meziane-Cherif; Arnaud Blondel; Patrice Courvalin; Michael Nilges; Thérèse E. Malliavin (J. Chem. Inf. Model., 2014)

ModBase, a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Benjamin M. Webb; Guang Qiang Dong; Dina Schneidman-Duhovny; Hao Fan 002; Seung Joong Kim; Natalia Khuri; Yannick G. Spill; Patrick Weinkam; Michal Hammel; John A. Tainer; Michael Nilges; et al. (Nucleic Acids Res., 2014)

An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps. - Guillaume Bouvier; Nathan Desdouits; Mathias Ferber; Arnaud Blondel; Michael Nilges (Bioinform., 2015)

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. - Andrea Cassioli; Benjamin Bardiaux; Guillaume Bouvier; Antonio Mucherino; Rafael Alves; Leo Liberti; Michael Nilges; Carlile Lavor; Thérèse E. Malliavin (BMC Bioinform., 2015)

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis. - Emna Harigua-Souiai; Isidro Cortes-Ciriano; Nathan Desdouits; Thérèse E. Malliavin; Ikram Guizani; Michael Nilges; Arnaud Blondel; Guillaume Bouvier (BMC Bioinform., 2015)

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. - Isidro Cortes-Ciriano; Gerard J. P. van Westen; Guillaume Bouvier; Michael Nilges; John P. Overington; Andreas Bender 002; Thérèse E. Malliavin (Bioinform., 2016)

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa: d-Lac Ligase VanA. - Nathalie Duclert-Savatier; Guillaume Bouvier; Michael Nilges; Thérèse E. Malliavin (J. Chem. Inf. Model., 2016)

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data. - Simeon Carstens; Michael Nilges; Michael Habeck (PLoS Comput. Biol., 2016)

Tuning interval Branch-and-Prune for protein structure determination. - Bradley Worley; Florent Delhommel; Florence Cordier; Thérèse E. Malliavin; Benjamin Bardiaux; Nicolas Wolff; Michael Nilges; Carlile Lavor; Leo Liberti (J. Glob. Optim., 2018)

Minimal NMR distance information for rigidity of protein graphs. - Carlile Lavor; Leo Liberti; Bruce Randall Donald; Bradley Worley; Benjamin Bardiaux; Thérèse E. Malliavin; Michael Nilges (Discret. Appl. Math., 2019)

mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics. - Damien Monet; Nathan Desdouits; Michael Nilges; Arnaud Blondel (J. Chem. Inf. Model., 2019)

ARIAweb: a server for automated NMR structure calculation. - Fabrice Allain; Fabien Mareuil; Hervé Ménager; Michael Nilges; Benjamin Bardiaux (Nucleic Acids Res., 2020)

The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators. - 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 (Bioinform., 2021)

Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology. - Hamed Khakzad; Lotta Happonen; Yasaman Karami; Sounak Chowdhury; Gizem Ertürk Bergdahl; Michael Nilges; Guy Tran Van Nhieu; Johan Malmström; Lars Malmström (PLoS Comput. Biol., 2021)

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions. - Vincent Mallet; Luis Checa Ruano; Alexandra Moine-Franel; Michael Nilges; Karen Druart; Guillaume Bouvier; Olivier Sperandio (Bioinform., 2022)

AlignScape, displaying sequence similarity using self-organizing maps. - Isaac Filella-Merce; Vincent Mallet; Eric Durand; Michael Nilges; Guillaume Bouvier; Riccardo Pellarin (Frontiers Bioinform., 2024)