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Quantifying the impact of scientific papers objectively is crucial for research output assessment, which subsequently affects institution and country rankings, research funding allocations, academic recruitment, and national/international scientific priorities. While most of the assessment schemes based on publication citations may potentially be manipulated through negative citations, in this paper, we explore the conflict of interest (COI) relationships and discover negative citations and subsequently weaken the associated citation strength. Positive and negative COIdistinguished objective rank algorithm (PANDORA) has been developed, which captures the positive and negative COI, together with the positive and negative suspected COI relationships. In order to alleviate the influence caused by negative COI relationship, collaboration times, collaboration time span, citation times, and citation time span are employed to determine the citing strength; while for positive COI relationship, we regard it as normal citation relationship. Furthermore, we calculate the impact of scholarly papers by PageRank and HITS algorithms, based on a credit allocation algorithm which is utilized to assess the impact of institutions fairly and objectively. Experiments are conducted on the publication data set from American Physical Society data set, and the results demonstrate that our method significantly outperforms the current solutions in recommendation intensity of list Rat top-K and Spearman's rank correlation coefficient at top-K.