As scientific and technological resources are experiencing information overload, it is quite expensive to find resources that users are interested in exactly. The personalized recommendation system is a good candidate to solve this problem, but data sparseness and the cold starting problem still prevent the application of the recommendation system. Sparse data affects the quality of the similarity measurement and consequently the quality of the recommender system. In this paper, we propose a matrix factorization recommendation algorithm based on similarity calculation(SCMF), which introduces potential similarity relationships to solve the problem of data sparseness. A penalty factor is adopted in the latent item similarity matrix calculation to capture more real relationships furthermore. We compared our approach with other 6 recommendation algorithms and conducted experiments on 5 public data sets. According to the experimental results, the recommendation precision can improve by 2% to 9% versus the traditional best algorithm. As for sparse data sets, the prediction accuracy can also improve by 0.17% to 18%. Besides, our approach was applied to patent resource exploitation provided by the wanfang patents retrieval system. Experimental results show that our method performs better than commonly used algorithms, especially under the cold starting condition.