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Computational and Structural Biotechnology Journal|June 30, 2026
Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein DesignJonathan Feldman, Maximilian Brogi, Jeffrey SkolnickBiorxiv : the Preprint Server for Biology|March 17, 2025
AF3Complex Yields Improved Structural Predictions of Protein ComplexesJonathan Feldman, Jeffrey SkolnickBioinformatics (Oxford, England)|July 31, 2025
AF3Complex yields improved structural predictions of protein complexesJonathan Feldman, Jeffrey SkolnickBiorxiv : the Preprint Server for Biology|May 4, 2026
AlphaInterp: Probing AlphaFold 3's Internal Representations Reveals Evolutionary Determinants of Predicted Structure and ConfidenceJonathan Feldman, Jeffrey SkolnickEmerging Topics in Life Sciences|February 2, 2021
Integrating the whole from the sum of the parts: vignettes in computational biologyJeffrey SkolnickCurrent Opinion in Structural Biology|March 10, 2006
In quest of an empirical potential for protein structure predictionJeffrey SkolnickThe Journal of Chemical Physics|September 17, 2016
Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromoleculesJeffrey SkolnickJournal of Chemical Information and Modeling|September 22, 2010
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screeningMichal Brylinski, Jeffrey SkolnickProceedings of the National Academy of Sciences of the United States of America|February 23, 2012
The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formationMu Gao, Jeffrey SkolnickProceedings of the National Academy of Sciences of the United States of America|January 18, 2005
The protein structure prediction problem could be solved using the current PDB libraryYang Zhang, Jeffrey SkolnickPageof 21