Services

Webserver and Downloads

1. Servers (! Due to security issues, the university has taken down these servers. They will not be available before the issues get fixed)
   • WebPDA for comprehensive analysis of protein-DNA complex structures¹
   • SCINDEL (Structural Comparison of Similar Proteins with Insertion and Deletion) for comparing protein structures with indels²
   • TFinDit for transcription factor-DNA interaction data depository
2. Downloads
   • PDA: Protein-DNA Complex Structure Analyze¹
   • Domainparser2: Automatic protein structural domain partition⁴
   • TF-DNA orientation-based interaction potential ⁵
3. Datasets
   • nr-indel dataset: 183 non-redundant indels²
   • Set263 and Cluster104 for the PDA paper¹

References:

1. Kim, R. and Guo, J-T. “PDA: an automatic and comprehensive analysis program for protein-DNA complex structures”, BMC Genomics, 10(Supple 1):S13, 2009
2. Kim, R. and Guo, J-T. “Systematic analysis of short internal indels and their impact on protein folding”, BMC Structural Biology, 10:24, 2010
3. Turner, D. Kim, R. Guo, J-T. “TFinDit: transcription factor-DNA interaction data depository”, BMC Bioinformatics,13:220, 2012
4. Guo, J-T. Kim, D. Xu, D. and Xu, Y. “Improving the Performance of DomainParser for Structural Domain Partition using Neural Network”, Nucleic Acids Research, 31(3):944-52.
5. Takeda, T. Corona, RI. Guo, J-T. “A knowledge-based orientation potential for transcription factor-DNA docking”, Bioinformatics, 29(3):322-30, 2013
6. Liu, Z.* Guo, J-T.* Li, T. Xu, Y. “Structure-based recognition of binding sites of transcription factors using an efficient protein-DNA docking approach”, Proteins: Structure, Function, and Bioinformatics, 72(4), 1114-1124, 2008
7. Corona RI. Sudarshan, S. Aluru, S. Guo, J-T*. “An SVM-based method for assessment of transcription factor-DNA complex models”, BMC Bioinformatics,19(suppl 20):506, 2018