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Current Opinion in Structural Biology|September 27, 2020
Systematic design of biomolecular force fieldsDavid van der SpoelJournal 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 ShehuBioengineering (Basel, Switzerland)|January 28, 2026
DyVarMap: Integrating Conformational Dynamics and Interpretable Machine Learning for Cancer-Associated Missense Variant Classification in FGFR2Yiyang Lian, Amarda ShehuMolecules (Basel, Switzerland)|January 20, 2018
From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure PredictionNasrin Akhter, Amarda ShehuProteome Science|July 5, 2012
Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surfaceBrian S Olson, Amarda ShehuPageof 19