Publications

Nabin Giri, Jianlin Cheng. De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. Nature Communications - GitHub.

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge - Nature Methods.

Nabin Giri, Liguo Wang, Jianlin Cheng. Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Nature Scientific Data - GitHub.

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment - PROTEINS: Structure, Function, and Bioinformatics - Results of 5th joint CASP-CAPRI protein assembly prediction challenge.

Raj S. Roy, Jian Liu, Nabin Giri, Zhiye Guo, Jianlin Cheng. Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15 - PROTEINS: Structure, Function, and Bioinformatics - Ranked 1st in CASP15 🎉.

Nabin Giri , Raj S. Roy, Jianlin Cheng. Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions - Current Opinion in Structural Biology.

Nabin Giri , Jianlin Cheng. Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge - Biomolecules - Feature Papers in Bioinformatics and Systems Biology Section.

Nabin Giri, Ashwin Dhakal, Jian Liu, Jianlin Cheng. Template-based Modeling for Accurate Prediction of Ligand-Protein Complex Structures in CASP15 - CASP15 Abstract Book.

Elham Soltanikazemi, Raj S. Roy, Farhan Quadir, Nabin Giri, Alex Morehead, Jianlin Cheng. DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning.

Gao, Mu, Peik Lund-Andersen, Alex Morehead, Sajid Mahmud, Chen Chen, Xiao Chen, Nabin Giri et al. High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function - 2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments (MLHPC).

My master’s thesis titled Recommendation System Using Factorization Model and MapReduce Framework is available here, the codes are available in GitHub repository, and to watch my three-minute thesis presentation please go here.