MutaProt: a web interface for structural analysis of point mutations. - Eran Eyal; Rafael Najmanovich; Vladimir Sobolev; Marvin Edelman (Bioinform., 2001)

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. - Eran Eyal; Rafael Najmanovich; Brendan J. McConkey; Marvin Edelman; Vladimir Sobolev (J. Comput. Chem., 2004)

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. - Richard J. Morris; Rafael Najmanovich; Abdullah Kahraman; Janet M. Thornton (Bioinform., 2005)

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. - Rafael Najmanovich; Abdellah Allali-Hassani; Richard J. Morris; Ludmila Dombrovsky; Patricia W. Pan; Masoud Vedadi; Alexander N. Plotnikov; Aled M. Edwards; Cheryl H. Arrowsmith; Janet M. Thornton (Bioinform., 2007)

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites. - Rafael Najmanovich; Natalja Kurbatova; Janet M. Thornton (ECCB, 2008)

Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site. - Valérie Campagna-Slater; Man Wai Mok; Kong T. Nguyen; Miklos Feher; Rafael Najmanovich; Matthieu Schapira (J. Chem. Inf. Model., 2011)

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. - Matthieu Chartier; Francis Gaudreault; Rafael Najmanovich (Bioinform., 2012)

Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding. - Francis Gaudreault; Matthieu Chartier; Rafael Najmanovich (Bioinform., 2012)

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. - Mathieu Larocque; Thierry Chénard; Rafael Najmanovich (BMC Syst. Biol., 2014)

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations. - Vincent Frappier; Rafael J. Najmanovich (PLoS Comput. Biol., 2014)

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID. - Francis Gaudreault; Louis-Philippe Morency; Rafael J. Najmanovich (Bioinform., 2015)

Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. - Ilan Samish; Philip E. Bourne; Rafael J. Najmanovich (Bioinform., 2015)

Detection of Binding Site Molecular Interaction Field Similarities. - Matthieu Chartier; Rafael Najmanovich (J. Chem. Inf. Model., 2015)

FlexAID: Revisiting Docking on Non-Native-Complex Structures. - Francis Gaudreault; Rafael J. Najmanovich (J. Chem. Inf. Model., 2015)

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability. - Vincent Frappier; Matthieu Chartier; Rafael J. Najmanovich (Nucleic Acids Res., 2015)

Parsing and model generation for biological processes. - Laouen Belloli; Gabriel A. Wainer; Rafael Najmanovich (SpringSim (TMS-DEVS), 2016)

IsoMIF Finder: online detection of binding site molecular interaction field similarities. - Matthieu Chartier; Etienne Adriansen; Rafael Najmanovich (Bioinform., 2016)

Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes. - Thierry Chénard; Frédéric Guénard; Marie-Claude Vohl; André Carpentier; André Tchernof; Rafael J. Najmanovich (BMC Syst. Biol., 2017)

The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes. - Olivier Mailhot; Rafael Najmanovich (Bioinform., 2021)

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. - Natália Teruel; Olivier Mailhot; Rafael J. Najmanovich (PLoS Comput. Biol., 2021)

SPEAR: Systematic ProtEin AnnotatoR. - Matthew Crown; Natália Teruel; Rafael Najmanovich; Matthew Bashton (Bioinform., 2022)

Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation. - Olivier Mailhot; Vincent Frappier; François Major; Rafael J. Najmanovich (PLoS Comput. Biol., 2022)

The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships. - Olivier Mailhot; François Major; Rafael Najmanovich (Bioinform., 2023)

Surfaces: a software to quantify and visualize interactions within and between proteins and ligands. - Natália Teruel; Vinicius Magalhães Borges; Rafael Najmanovich (Bioinform., 2023)

Understanding and Predicting Ligand Efficacy in the μ-Opioid Receptor through Quantitative Dynamical Analysis of Complex Structures. - Gabriel T. Galdino; Olivier Mailhot; Rafael Najmanovich (J. Chem. Inf. Model., 2024)