Author

Shivaram Danwada

Auburn University at Montgomery

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:protein sequence· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:protein structure prediction· 1

Frequent Co-Authors

Cheryl SealsiD· 2 shared Nilanjana RaychawdharyiD· 2 shared Priscilla Udomprasert· 2 shared Sutanu BhattacharyaiD· 2 shared Lei Wu· 1 shared Robert Spicer· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 14 mutual co-author links

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2 shared papersBioinformatics

Cheryl SealsORCID

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2 papers

Recent·Most cited

Evaluating Protein Language Model Embeddingsfor Structural Similarity in the Protein-Sequence Twilight Zone

Shivaram Danwada, Priscilla Udomprasert, Nilanjana Raychawdhary, Cheryl Seals, Lei Wu, Sutanu Bhattacharya

This study evaluates protein language model embeddings for estimating structural similarity in the protein-sequence twilight zone and finds that ProstT5 performs best.

bioRxiv · Jul 31, 2026 · PreprintBioinformatics

Evaluating the Significance of Embedding-Based Protein Sequence Alignment with Clustering and Double Dynamic Programming for Remote Homology

Robert Spicer, Nilanjana Raychawdhary, Shivaram Danwada, Priscilla Udomprasert, Cheryl Seals, Sutanu Bhattacharya

This study evaluates an embedding-based protein sequence alignment method using clustering and double dynamic programming, showing improved performance in detecting remote homology compared to traditional and state-of-the-art approaches.

Scientific Reports · Nov 12, 2025Peer-reviewedBioinformatics