Contact Us
Contact Information
The software is free to academic users ONLY; For commercial usage, please contact with us(Xiaoyong Pan,2008xypan@sjtu.edu.cn)
Address
Shanghai Jiao Tong University, Shanghai, China
Frequently Asked Questions
How do I use AlignIF?
Check our Read Me page for detailed instructions on using the tool.
What happens if my input PDB file contains proteins or ligands?
AlignIF automatically extracts RNA chains and ignores proteins/DNA/ligands. However, if the RNA structure is heavily influenced by protein binding, consider providing a standalone RNA structure for best results.
How do I interpret the sequence logo in the results?
The sequence logo visualizes conserved nucleotides across designed sequences: Tall letters = highly conserved positions (important for maintaining structure). Short letters = variable positions (more flexible in sequence design).