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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 ShehuProteome Science|February 26, 2014
HopDock: a probabilistic search algorithm for decoy sampling in protein-protein dockingIrina Hashmi, Amarda ShehuJournal of Bioinformatics and Computational Biology|July 20, 2012
An evolutionary conservation-based method for refining and reranking protein complex structuresBahar Akbal-Delibas, Irina Hashmi, Amarda Shehu, et al.Journal of Bioinformatics and Computational Biology|July 20, 2012
Guiding protein docking with geometric and evolutionary informationIrina Hashmi, Bahar Akbal-Delibas, Nurit Haspel, et al.IEEE 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 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 ShehuPageof 8