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Avinash Sreedasyam

dblp:140/4981 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
0000-0001-7336-7012ORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
protein structure prediction
0.712023
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023
Bioinformatics and computational biology › proteomics
structural proteomics
0.712023
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023
Bioinformatics and computational biology › protein function prediction › enzyme function prediction
enzyme classification
0.212023
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

structural alignment · 0.7alphafold · 0.7
YearPublicationVenuePosition
2023 Predicted structural proteome of Sphagnum divinum and proteome-scale annotation
abstract
MOTIVATION: Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. RESULTS: We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation. AVAILABILITY AND IMPLEMENTATION: All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.
Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova
Bioinform.5