Protein Databases

Latest research

1. Black pepper knowledge base (BlackPepKB): a centralized web resource for functional genomics of black pepper (Piper nigrum L.)

   • L. M. D. Bawanga
   • D. R. R. Wijewardene
   • Anushka M. Wickramasuriya

   in BMC Genomics

   Article Open access 17 October 2025

   

2. Empathi: embedding-based phage protein annotation tool by hierarchical assignment

   • Alexandre Boulay
   • Audrey Leprince
   • Clovis Galiez

   in Nature Communications

   Article Open access 14 October 2025

   

3. ProFlex as a linguistic bridge for decoding protein dynamics in normal mode analysis

   • Damian J. Magill
   • Timofey A. Skvortsov

   in Nature Communications

   Article Open access 13 October 2025

   

4. JinhuaNSICU, an open accessible Neurosurgical Intensive Care Database

   • Lin Chen
   • Ziyi Huang
   • Minfeng Tong

   in Scientific Data

   Article Open access 09 October 2025

   

5. ‘Google for DNA’ brings order to biology’s big data

   • Elie Dolgin

   in Nature

   Article 08 October 2025

   

6. Efficient and accurate search in petabase-scale sequence repositories

   • Mikhail Karasikov
   • Harun Mustafa
   • André Kahles

   in Nature

   Article Open access 08 October 2025

   

7. AI-driven protein pocket detection through integrating deep Q-networks for structural analysis

   • Prashanth Choppara
   • Lokesh Bommareddy

   in Journal of Computer-Aided Molecular Design

   Article 06 October 2025

   

8. Amyloid-β, Tau, and α-Synuclein Protein Interactomes as Therapeutic Targets in Neurodegenerative Diseases

   • D. Mohan Kumar
   • Priti Talwar

   in Cellular and Molecular Neurobiology

   Article Open access 06 October 2025

   

9. A library of avian proteins improves palaeoproteomic taxonomic identification and reveals widespread intraspecies variability

   • Maria C. Codlin
   • Lisa Yeomans
   • Beatrice Demarchi

   in Nature Communications

   Article Open access 03 October 2025

   

10. Proteoform search from protein database with top-down mass spectra

    • Kunyi Li
    • Baozhen Shan
    • Lusheng Wang

    in Nature Computational Science

    Article 03 October 2025

    

11. GENEOnet: a breakthrough in protein binding pocket detection using group equivariant non-expansive operators

    • Giovanni Bocchi
    • Patrizio Frosini
    • Carmine Talarico

    in Scientific Reports

    Article Open access 03 October 2025

    

12. Model organism databases face budget cuts and closures

    • Amanda Heidt

    in Nature

    Article 02 October 2025

    

13. Machine learning framework to extract physicochemical features of B-cell epitopes recognized by a cross-reactive antibody

    • Simranjit Grewal
    • Uwa Iyamu
    • Stephanie K. Yanow

    in npj Systems Biology and Applications

    Article Open access 02 October 2025

    

14. A trimodal protein language model enables advanced protein searches

    • Jin Su
    • Yan He
    • Fajie Yuan

    in Nature Biotechnology

    Article 02 October 2025

    

15. Protein sequence-based classification of Alzheimer’s disease using deep learning and attention mechanism

    • Bornali Baruah
    • Anindya Halder
    • Ansuman Kumar

    in Iran Journal of Computer Science

    Article 30 September 2025

    

16. BIRDBASE: A Global Dataset of Avian Biogeography, Conservation, Ecology and Life History Traits

    • Çağan H. Şekercioğlu
    • Kyle D. Kittelberger
    • Montague H. C. Neate-Clegg

    in Scientific Data

    Article Open access 30 September 2025

    

17. PaRPI predicts RNA-Protein interactions from cross-protocol and cross-batch RNA-binding protein datasets

    • Liangchen Peng
    • Lijun Quan
    • Qiang Lyu

    in Communications Biology

    Article Open access 30 September 2025

    

18. TumorXDB: an integrated multi-omics xWAS/xQTL platform for cross-ethnic pan-cancer analysis

    • Zehua Dong
    • Yihang Cheng
    • Deqiang Sun

    in Journal of Translational Medicine

    Article Open access 30 September 2025

    

19. CPMOAD: comprehensive preeclampsia multi-omics analysis database

    • Yang Fang
    • Mengzhe Fan
    • Linlin Zhang

    in Journal of Translational Medicine

    Article Open access 30 September 2025

    

20. SARST2 high-throughput and resource-efficient protein structure alignment against massive databases

    • Wei-Cheng Lo
    • Arieh Warshel
    • Shih-Wen Weng

    in Nature Communications

    Article Open access 30 September 2025

    

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