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Plos Computational Biology|September 2, 2015
Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary AlgorithmRudy Clausen, Buyong Ma, Ruth Nussinov, et al.Molecules (Basel, Switzerland)|February 15, 2019
Computational Structural Biology: Successes, Future Directions, and ChallengesRuth Nussinov, Chung-Jung Tsai, Amarda Shehu, et al.Biomolecules|July 27, 2022
Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound AntibodyKazi Lutful Kabir, Buyong Ma, Ruth Nussinov, et al.Plos Computational Biology|April 29, 2016
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsTatiana Maximova, Ryan Moffatt, Buyong Ma, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 30, 2015
idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein DockingIrina Hashmi, Amarda ShehuIEEE Transactions on Nanobioscience|February 11, 2016
A General, Adaptive, Roadmap-Based Algorithm for Protein Motion ComputationKevin Molloy, Amarda ShehuJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|July 24, 2015
A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy LandscapesRudy Clausen, Amarda ShehuProteome Science|February 26, 2014
HopDock: a probabilistic search algorithm for decoy sampling in protein-protein dockingIrina Hashmi, Amarda ShehuBMC Structural Biology|February 26, 2014
Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired methodKevin Molloy, Amarda ShehuBiomolecules|November 24, 2022
GOProFormer: A Multi-Modal Transformer Method for Gene Ontology Protein Function PredictionAnowarul Kabir, Amarda ShehuPageof 69