Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. - Ryan Brenke; Dima Kozakov; Gwo-Yu Chuang; Dmitri Beglov; David R. Hall; Melissa R. Landon; Carla Mattos; Sandor Vajda (Bioinform., 2009)

Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. - Melissa R. Landon; Raquel L. Lieberman; Quyen Q. Hoang; Shulin Ju; Jose M. M. Caaveiro; Susan D. Orwig; Dima Kozakov; Ryan Brenke; Gwo-Yu Chuang; Dmitri Beglov; Sandor Vajda; Gregory A. Petsko; et al. (J. Comput. Aided Mol. Des., 2009)

A new approach to rigid body minimization with application to molecular docking. - Hanieh Mirzaei; Dima Kozakov; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Pirooz Vakili (CDC, 2012)

Application of asymmetric statistical potentials to antibody-protein docking. - Ryan Brenke; David R. Hall; Gwo-Yu Chuang; Stephen R. Comeau; Tanggis Bohnuud; Dmitri Beglov; Ora Schueler-Furman; Sandor Vajda; Dima Kozakov (Bioinform., 2012)

FTMAP: extended protein mapping with user-selected probe molecules. - Chi-Ho Ngan; Tanggis Bohnuud; Scott E. Mottarella; Dmitri Beglov; Elizabeth A. Villar; David R. Hall; Dima Kozakov; Sandor Vajda (Nucleic Acids Res., 2012)

Flexible refinement of protein-ligand docking on manifolds. - Hanieh Mirzaei; Elizabeth A. Villar; Scott E. Mottarella; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov; Pirooz Vakili (CDC, 2013)

FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. - Laurie E. Grove; David R. Hall; Dmitri Beglov; Sandor Vajda; Dima Kozakov (Bioinform., 2013)

Docking Server for the Identification of Heparin Binding Sites on Proteins. - Scott E. Mottarella; Dmitri Beglov; Natalia Beglova; Matthew A. Nugent; Dima Kozakov; Sandor Vajda (J. Chem. Inf. Model., 2014)

ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. - Kathryn A. Porter; Bing Xia; Dmitri Beglov; Tanggis Bohnuud; Nawsad Alam; Ora Schueler-Furman; Dima Kozakov (Bioinform., 2017)

Protein-ligand docking using FFT based sampling: D3R case study. - Dzmitry Padhorny; David R. Hall; Hanieh Mirzaei; Artem B. Mamonov; Mohammad Moghadasi; Andrey Alekseenko; Dmitri Beglov; Dima Kozakov (J. Comput. Aided Mol. Des., 2018)

Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. - Amanda E. Wakefield; Christine Yueh; Dmitri Beglov; Marcelo Santos Castilho; Dima Kozakov; György M. Keserü; Adrian Whitty; Sandor Vajda (J. Chem. Inf. Model., 2020)

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. - Omeir Khan; George Jones; Maria Lazou; Diane Joseph-McCarthy; Dima Kozakov; Dmitri Beglov; Sandor Vajda (J. Chem. Inf. Model., 2024)