Protein Databases

Latest research

1. 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

   

2. RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets

   • Luisa Hemm
   • Dominik Rabsch
   • Rolf Backofen

   in Nature Communications

   Article Open access 26 September 2025

   

3. Unravelling the Phosphorylation Landscape of Anthrax Toxin Receptor 1: Mechanisms and Functional Insights Through Phosphoproteomic Data Integration

   • Ayadathil Sujina
   • Amal Fahma
   • Rajesh Raju

   in The Protein Journal

   Article 26 September 2025

   

4. OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data

   • Ali Yazdizadeh Kharrazi
   • Adrian M. Altenhoff
   • Sina Majidian

   in Journal of Molecular Evolution

   Article 26 September 2025

   

5. S-100B in acute ischemic stroke: a visualization of global hotspots

   • Samhitha Gurijala
   • Sofia Malik
   • Latha Ganti

   in International Journal of Emergency Medicine

   Article Open access 26 September 2025

   

6. Facilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant

   • Walter Viegener
   • Shamil Urazbakhtin
   • Jinqiu Xiao

   in Nature Communications

   Article Open access 25 September 2025

   

7. NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes

   • Dong-Ha Oh
   • Alexander Astashyn
   • Vamsi K. Kodali

   in Journal of Molecular Evolution

   Article Open access 25 September 2025

   

8. Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences

   • Taner Karagöl
   • Alper Karagöl
   • Shuguang Zhang

   in Journal of Molecular Evolution

   Article Open access 24 September 2025

   

9. A Localized GTEx Database and Its Potential Applications in Biomedical Research

   • G. A. Churakov
   • M. D. Belyakov
   • S. V. Orlov

   in Molecular Biology

   Article 22 September 2025

   

10. Proteomic analysis and functional characterization of excretory-secretory products from adult Toxocara canis: insights into parasite–host interactions

    • Ya-Jia Zhou
    • Zhi-Yu Li
    • Wen-Bin Zheng

    in BMC Genomics

    Article Open access 22 September 2025

    

11. Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA

    • Yaohui Chen
    • Jung-Hyun Kim
    • Ramaiah Nagaraja

    in Journal of Molecular Evolution

    Article Open access 19 September 2025

    

12. GPU-accelerated homology search with MMseqs2

    • Felix Kallenborn
    • Alejandro Chacon
    • Martin Steinegger

    in Nature Methods

    Article Open access 18 September 2025

    

13. Ecological risk assessment for Cry1Da_7, Cry1B.3 and Vip3Cb1 proteins expressed in MON 89151 cotton: an insect-protected cotton with targeted activity against Lepidoptera

    • Harit K. Bal
    • Collin J. Preftakes
    • Christopher R. Brown

    in Transgenic Research

    Article Open access 16 September 2025

    

14. Unraveling cooperative and competitive interactions within protein triplets in the human interactome

    • Aimilia-Christina Vagiona
    • Pablo Mier
    • Miguel A. Andrade-Navarro

    in Scientific Reports

    Article Open access 15 September 2025

    

15. Unveiling the Evolutionary History and Functional Significance of the Protein Z-Dependent Protease Inhibitor (ZPI) Across Vertebrates

    • Chennakesavan Suganthi
    • Parthiban Akshayaa
    • Narayanan Manoj

    in Journal of Molecular Evolution

    Article 15 September 2025

    

16. MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes

    • Guo Ye
    • Hao Hong
    • Tao Li

    in Genome Biology

    Article Open access 10 September 2025

    

17. Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools

    • Mohsin Shad
    • Ayesha Liaqat
    • Muhammad Sajjad

    in Applied Biochemistry and Biotechnology

    Article 09 September 2025

    

18. Combining knowledge distillation and neural networks to predict protein secondary structure

    • Lufei Zhao
    • Jingyi Li
    • Xuchu Jiang

    in Scientific Reports

    Article Open access 31 August 2025

    

19. A survey of computational tools for heterochiral proteins

    • Francesco Grandolfo
    • Savino Longo

    in Rendiconti Lincei. Scienze Fisiche e Naturali

    Article Open access 30 August 2025

    

20. Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence

    • Jamie Canderan
    • Moses Stamboulian
    • Yuzhen Ye

    in Health Information Science and Systems

    Article Open access 29 August 2025

    

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