Publications

45 journal, preprint and conference papers by Michel Sanner and colleagues, newest first.

2025

• Sulfoxide-diazirine (SODA) as a Cleavable Photoaffinity Group To Enable the Identification of Photolabeled Modification Sites via LC–MS³
  Suyuan Chen, Michel F. Sanner, Denise-Liu′ Gracias Leone, Stefan Loroch, Stefano Forli, Steven H. L. Verhelst. Analytical Chemistry (2025).

2023

• Docking Peptides into HIV/FIV Protease with Deep Learning and Focused Peptide Docking Methods
  Katherine Ge, Dayna Olson, Michel F. Sanner. arXiv (2023).
• Predicting Protein–Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking
  Sudhanshu Shanker, Michel F. Sanner. Journal of Chemical Information and Modeling (2023).

2021

• Improving Docking Power for Short Peptides Using Random Forest
  Michel F. Sanner, Leonard Dieguez, Stefano Forli, Ewa Lis. Journal of Chemical Information and Modeling (2021).
• Cyclic Peptides as Protein Kinase Inhibitors: Structure–Activity Relationship and Molecular Modeling
  Michel F. Sanner, Khalid Zoghebi, Samara Hanna, Saghar Mozaffari, Simin Rahighi, Rakesh K. Tiwari, Keykavous Parang. Journal of Chemical Information and Modeling (2021).
• Accelerating AutoDock4 with GPUs and Gradient-Based Local Search
  Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas F Tillack, Michel F Sanner, Andreas Koch, Stefano Forli. Journal of Chemical Theory and Computation (2021).

2020

• The AutoDock suite at 30
  David S. Goodsell, Michel F. Sanner, Arthur J. Olson, Stefano Forli. Protein Science (2020).
• C‐terminal residues of activated protein C light chain contribute to its anticoagulant and cytoprotective activities
  Atsuki Yamashita, Yuqi Zhang, Michel F. Sanner, John H. Griffin, Laurent O. Mosnier. Journal of Thrombosis and Haemostasis (2020).

2019

• Docking Flexible Cyclic Peptides with AutoDock CrankPep
  Yuqi Zhang, Michel F. Sanner. Journal of Chemical Theory and Computation (2019).
• AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools
  Yuqi Zhang, Stefano Forli, Anna Omelchenko, Michel F. Sanner. Journal of Computational Chemistry (2019).
• AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes
  Yuqi Zhang, Michel F Sanner. Bioinformatics (2019).

2017

• Activated protein C light chain provides an extended binding surface for its anticoagulant cofactor, protein S
  José A. Fernández, Xiao Xu, Ranjeet K. Sinha, Laurent O. Mosnier, Michel F. Sanner, John H. Griffin. Blood Advances (2017).

2016

• AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms
  Pradeep Anand Ravindranath, Michel F. Sanner. Bioinformatics (2016).
• Computational protein–ligand docking and virtual drug screening with the AutoDock suite
  Stefano Forli, Ruth Huey, Michael E Pique, Michel F Sanner, David S Goodsell, Arthur J Olson. Nature Protocols (2016).

2015

• AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
  Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner. PLOS Computational Biology (2015).

2014

• cellPACK: a virtual mesoscope to model and visualize structural systems biology
  Graham T Johnson, Ludovic Autin, Mostafa Al-Alusi, David S Goodsell, Michel F Sanner, Arthur J Olson. Nature Methods (2014).
• 3D molecular models of whole HIV-1 virions generated with cellPACK
  Graham T. Johnson, David S. Goodsell, Ludovic Autin, Stefano Forli, Michel F. Sanner, Arthur J. Olson. Faraday Discuss. (2014).

2013

• Protein-Protein Docking with F2Dock 2.0 and GB-Rerank
  Rezaul Chowdhury, Muhibur Rasheed, Donald Keidel, Maysam Moussalem, Arthur Olson, Michel Sanner, Chandrajit Bajaj. PLoS ONE (2013).

2012

• uPy: A Ubiquitous CG Python API with Biological-Modeling Applications
  L. Autin, G. Johnson, J. Hake, A. Olson, M. Sanner. IEEE Computer Graphics and Applications (2012).

2011

• ePMV Embeds Molecular Modeling into Professional Animation Software Environments
  Graham T. Johnson, Ludovic Autin, David S. Goodsell, Michel F. Sanner, Arthur J. Olson. Structure (2011).

2009

• Derivation of a Retinoid X Receptor Scaffold from Peroxisome Proliferator‐Activated Receptor γ Ligand 1‐Di(1H‐indol‐3‐yl)methyl‐4‐trifluoromethylbenzene
  Marcia I. Dawson, Mao Ye, Xihua Cao, Lulu Farhana, Qiong‐Ying Hu, Yong Zhao, Li Ping Xu, Alice Kiselyuk, Ricardo G. Correa, Li Yang, Tingjun Hou, John C. Reed, Pamela Itkin‐Ansari, Fred Levine, Michel F. Sanner, Joseph A. Fontana, Xiao‐Kun Zhang. ChemMedChem (2009).
• AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
  Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson. Journal of Computational Chemistry (2009).

2008

• Shape complementarity of protein–protein complexes at multiple resolutions
  Qing Zhang, Michel Sanner, Arthur J. Olson. Proteins: Structure, Function, and Bioinformatics (2008).

2007

• Protein–ligand docking with multiple flexible side chains
  Yong Zhao, Michel F. Sanner. Journal of Computer-Aided Molecular Design (2007).
• A dynamical study of antibody–antigen encounter reactions
  Lorenzo Bongini, Duccio Fanelli, Francesco Piazza, Paolo De Los Rios, Michel Sanner, Ulf Skoglund. Physical Biology (2007).
• FLIPDock: Docking flexible ligands into flexible receptors
  Yong Zhao, Michel F. Sanner. Proteins: Structure, Function, and Bioinformatics (2007).

2006

• Hierarchical and multi-resolution representation of protein flexibility
  Yong Zhao, Daniel Stoffler, Michel Sanner. Bioinformatics (2006).

2005

• Tangible Augmented Interfaces for Structural Molecular Biology
  A. Gillet, M. Sanner, D. Stoffler, A. Olson. IEEE Computer Graphics and Applications (2005).
• A Component-Based Software Environment for Visualizing Large Macromolecular Assemblies
  Michel F. Sanner. Structure (2005).
• Tangible Interfaces for Structural Molecular Biology
  Alexandre Gillet, Michel Sanner, Daniel Stoffler, Arthur Olson. Structure (2005).
• Visualizing Nature at Work from the Nano to the Macro Scale
  Michel F. Sanner, Martin Stolz, Peter Burkhard, Xiang-Peng Kong, Guangwei Min, Tung-Tien Sun, Sergey Driamov, Ueli Aebi, Daniel Stoffler. Nanobiotechnology (2005).

2002

• Model of the αLβ2 integrin I‐domain/ICAM‐1 DI interface suggests that subtle changes in loop orientation determine ligand specificity
  Glen B. Legge, Garrett M. Morris, Michel F. Sanner, Yoshikazu Takada, Arthur J. Olson, Flavio Grynszpan. Proteins: Structure, Function, and Bioinformatics (2002).
• Evolutionary analysis of HIV‐1 protease inhibitors: Methods for design of inhibitors that evade resistance
  Daniel Stoffler, Michel F. Sanner, Garrett M. Morris, Arthur J. Olson, David S. Goodsell. Proteins: Structure, Function, and Bioinformatics (2002).
• ViPEr, a Visual Programming Environment for Python
  Michel F. Sanner, Daniel Stoffler, Arthur J. Olson. Proceedings of the 10th International Python Conference (Python 10) (2002). Best paper award

2001

• Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
  Fredrik Österberg, Garrett M. Morris, Michel F. Sanner, Arthur J. Olson, David S. Goodsell. Proteins: Structure, Function, and Bioinformatics (2001).

1999

• The discovery of steroids and other novel FKBP inhibitors using a molecular docking program
  P. Burkhard, U. Hommel, M. Sanner, M.D. Walkinshaw. Journal of Molecular Biology (1999).
• Python: a programming language for software integration and development.
  M F Sanner. Journal of molecular graphics & modelling (1999).

1997

• Recognition of protein structure on coarse lattices with residue- residue energy functions
  B. A. Reva, A. V. Finkelstein, M. Sanner, A. J. Olson, J. Skolnick. Protein Engineering Design and Selection (1997).
• Residue-residue mean-force potentials for protein structure recognition
  B. A. Reva, A. V. Finkelstein, M. F. Sanner, A. J. Olson. Protein Engineering Design and Selection (1997).
• Design and Synthesis of Transition State Analogs for Induction of Hydride Transfer Catalytic Antibodies
  Josef Schröer, Michel Sanner, Jean-Louis Reymond. The Journal of Organic Chemistry (1997).

1996

• Adjusting potential energy functions for lattice models of chain molecules
  Boris A. Reva, Alexei V. Finkelstein, Michel F. Sanner, Arthur J. Olson. Proteins: Structure, Function, and Genetics (1996).
• Lattice modeling: Accuracy of energy calculations
  Boris A. Reva, Michel F. Sanner, Arthur J. Olson, Alexei V. Finkelstein. Journal of Computational Chemistry (1996).
• Reduced surface: An efficient way to compute molecular surfaces
  Michel F. Sanner, Arthur J. Olson, Jean-Claude Spehner. Biopolymers (1996).

1990

• Conformational studies of cyclic peptide structures in solution from ¹H‐Nmr data by distance geometry calculation and restrained energy minimization
  Hans Senn, Hans‐Rudolf Loosli, Michel Sanner, Werner Braun. Biopolymers (1990).

1989

• GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data
  Michel Sanner, Armin Widmer, Hans Senn, Werner Braun. Journal of Computer-Aided Molecular Design (1989).