R. Ashizawa, S. Kotelnikov, O. Khan, et al., Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16 , Proteins: Structure, Function, and Bioinformatics 94, no. 1 2026 : 183–191,  doi

Jones G, Jindal A, Ghani U, Kotelnikov S, Egbert M, Hashemi N, Vajda S, Padhorny D, Kozakov D. Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap.Acta Crystallogr D Struct Biol. 2022 Jun 1;78(Pt 6):690-697.  doi

Desta IT, Porter KA, Xia B, Kozakov D, Vajda S. Performance and Its Limits in Rigid Body Protein-Protein Docking. Structure. 2020 Sep; 28 (9):1071-1081.  doi

Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New additions to the ClusPro server motivated by CAPRI. Proteins: Structure, Function, and Bioinformatics. 2017 Mar; 85(3):435-444.  pdf

Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nature Protocols. 2017 Feb;12(2):255-278. pdf

Kozakov D, Beglov D, Bohnuud T, Mottarella S, Xia B, Hall DR, Vajda, S. How good is automated protein docking? Proteins: Structure, Function, and Bioinformatics. 2013 Dec; 81(12):2159-66.  pdf

For Peptide mode:

Porter KA, Xia B, Beglov D, Bohnuud T, Alam N, Schueler-Furman O, Kozakov D.ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT. Bioinformatics. 2017 Oct; 33(20):3299-3301. pdf

For Dimer Classification mode:

Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking. Journal of Molecular Biology. 2017 Feb; 429(3):372-381. pdf

For Antibody mode:

Brenke R, Hall DR, Chuang G-Y, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics. 2012 Oct; 28(20):2608-2614;  pdf

For Restraints mode:

Xia B, Vajda S, Kozakov D. Accounting for pairwise distance restraints in FFT-based protein–protein docking. Bioinformatics. 2016 Nov; 32(21): 3342-3344. pdf

For SAXS mode:

Ignatov M, Kazennov A, Kozakov D. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. Journal of Molecular Biology. 2018 Jul; 430(15):2249-2255. link

and

Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis IC, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro. Journal of Computational Chemistry. 2015 Jun.36(20):1568-1572. pdf