An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported.

HMGB4 protein which was identified in 2008 is a member of mammalian non-histone HMGB protein family. All HMGB proteins bind to DNA through two tandem DNAbinding motifs named HMG-box A and HMG-box B. HMGB proteins are known to improve the anticancer properties of platinum-based drugs such as cisplatin by high affinity binding to the platinum-DNA adducts and retarding the process of DNA excision repair. The results from previous studies have revealed in comparison with full-length HMGB1, the full-length HMGB4 binds with higher affinity to platinum-DNA lesions and inhibits the excision repair of the lesions much more efficient. It seems the hypersensitivity of testicular germ cell tumors to cisplatin is originated from strong expression of HMGB4 in this tissue. In the present work, the tertiary structure of human HMGB4 was determined using two methods based on homology modeling (Modeller software and I-TASSER server). The results show that models created by both methods have good quality and stability. Although I-TASSER model in comparison to the Modeller better explain the differences between HMGB1 and HMGB4 binding to the platinated DNA. The results obtained from the work demonstrate that HMGB4 binds to DNA by intercalating of Valine17 and Phenylalanine38 from box A and Leucine101 and Valine120 from box B between base pairs of DNA minor groove. The results also show the C-terminal part of HMGB4 possesses disordered tertiary structure. In general, the results will be helpful to understand the structure-function relationship of the protein and to design new anticancer drugs.