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Proceedings of the National Academy of Sciences of the United States of America|July 23, 2004
Anchor residues in protein-protein interactionsDeepa Rajamani, Spencer Thiel, Sandor Vajda, et al.
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference|October 20, 2007
Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnelsIoannis Ch Paschalidis, Yang Shen, Pirooz Vakili, et al.
Plos Computational Biology|October 11, 2008
Protein docking by the underestimation of free energy funnels in the space of encounter complexesYang Shen, Ioannis Ch Paschalidis, Pirooz Vakili, et al.
IEEE Transactions on Automatic Control|September 18, 2009
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein DockingIoannis Ch Paschalidis, Yang Shen, Pirooz Vakili, et al.
Biorxiv : the Preprint Server for Biology|January 8, 2026
The Influence of Ligands on AlphaFold3 Prediction of Cryptic PocketsMaria Lazou, Felix Tuchscherer, Sandor Vajda, et al.
Communications Biology|July 7, 2026
The influence of ligands on AlphaFold3 prediction of cryptic pocketsMaria Lazou, Felix Tuchscherer, Sandor Vajda, et al.
Biochemistry|January 26, 2005
Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mappingShu-Hsien Sheu, Taner Kaya, David J Waxman, et al.
Chemical Research in Toxicology|August 22, 2006
Computational screening of phthalate monoesters for binding to PPARgammaTaner Kaya, Scott C Mohr, David J Waxman, et al.
Proteins|April 16, 2003
Algorithms for computational solvent mapping of proteinsTamas Kortvelyesi, Sheldon Dennis, Michael Silberstein, et al.
Proteins|November 25, 2003
Combination of scoring functions improves discrimination in protein-protein dockingJohn Murphy, David W Gatchell, Jahnavi C Prasad, et al.
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