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Using gastric cancer phage display library, a novel anti-human gastric cancer scFv, named as SC1 was screened. The SC1 gene was constructed and expressed in E.Coli. After sequencing, the heavy and light chain variable region of SC1 (named as SC1VH and SC1VL, respectively) was modeled using computer-guided modeling method. With molecular docking method, the 3-D complex structure of SC1VH and SC1VL, i.e. Fv fragment of SC1, was constructed and optimized with molecular dynamics method. Choosing the common linker (GGGGS)3, the 3-D structure of SC1 was constructed and analyzed. The determination and analysis of the primary and 3-D structures of SC1 highlights the further human gastric cancer diagnosis and therapy.