Welcome to StoneMod

Kidney stone disease (nephrolithiasis) is an ancient and common affliction. It has been recognized for a long time with evidence of stone found in approximately 7,000-year-old mummies. However, it remains a global public health problem with increasing incidence/prevalence, reflecting ineffective prevention and poor understanding of the disease pathogenesis. Therefore, stone research during the past few decades has attempted to address mechanisms of kidney stone formation at tissue, cellular, subcellular and molecular levels. One aspect of such research that draws lots of attention from many researchers is the study on crystal modulation with the ultimate goals to better understand the processes of crystallization, crystal growth, crystal aggregation, and crystal adhesion to renal tubular cells, which are essential for kidney stone formation, and to define strategy to inhibit these processes.

In the urine and kidney tissues, there are a group of molecules, including proteins, which can modulate kidney stone formation by either promoting or inhibiting each step of the stone formation processes. Unfortunately, these lines of references had been previously dispersed. It is thus essential to generate a resource or database for kidney stone modulators that allows researchers to rapidly and accurately obtain precise information of the existing modulators and their effects on kidney stone formation.

References:

• Thongboonkerd V. Proteomics and kidney stone disease. Contrib Nephrol. 2008;160:142-58. doi: 10.1159/000125972. [PMID: 18401167]

• Vinaiphat A, Thongboonkerd V. Prospects for proteomics in kidney stone disease. Expert Rev Proteomics. 2017 Mar;14(3):185-187. [PMID: 28092479]

• Thongboonkerd V. Proteomics of Crystal-Cell Interactions: A Model for Kidney Stone Research. Cells. 2019;8(9). [PMID: 31547429]

• Sassanarakkit S, Peerapen P, Thongboonkerd V. StoneMod: a database for kidney stone modulatory proteins with experimental evidence. Sci Rep. 2020;10(1):15109. [PMID: 32934277]

• Peerapen P, Thongboonkerd V. Kidney stone proteomics: an update and perspectives. Expert Rev Proteomics. 2021;18(7):557-69. [PMID: 34320328]

• Yoodee S, Thongboonkerd V. Bioinformatics and computational analyses of kidney stone modulatory proteins lead to solid experimental evidence and therapeutic potential. Biomed Pharmacother. 2023;159:114217. [PMID: 36623450]

• Peerapen P, Thongboonkerd V. Protein network analysis and functional enrichment via computational biotechnology unravel molecular and pathogenic mechanisms of kidney stone disease. Biomed J. 2023;46(2):100577. [PMID: 36642221]

• Peerapen P, Thongboonkerd V. Kidney Stone Prevention. Adv Nutr. 2023;14(3):555-69. [PMID: 36906146]

• Sassanarakkit S, Peerapen P, Thongboonkerd V. OxaBIND: A tool for identifying oxalate-binding domain(s)/motif(s) in protein(s). Int J Biol Macromol. 2023;243:125275. [PMID: 37301337]

• Sassanarakkit S, Peerapen P, Thongboonkerd V. StoneMod 2.0: Database and prediction of kidney stone modulatory proteins. Int J Biol Macromol. 2024:129912.[PMID:38309384]