GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison

Ma, Chao; Wang, Lirong; Xie, Xiang‐Qun

doi:10.1021/ci1004948

Cited by 74 publications

(63 citation statements)

References 22 publications

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“…Given that molecule with Caco-2 value less than −0.4 is not permeable, the threshold of Caco-2 permeability was set to −0.4. Database-dependent DL evaluation approach based on Tanimoto coefficient78 was applied and shown as follows.…”

Section: Methodsmentioning

confidence: 99%

Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach

Yue

Xin

Fan

et al. 2017

Sci Rep

113

119

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Herb pair Danggui-Honghua has been frequently used for treatment of blood stasis syndrome (BSS) in China, one of the most common clinical pathological syndromes in traditional Chinese medicine (TCM). However, its therapeutic mechanism has not been clearly elucidated. In the present study, a feasible system pharmacology model based on chemical, pharmacokinetic and pharmacological data was developed via network construction approach to clarify the mechanisms of this herb pair. Thirty-one active ingredients of Danggui-Honghua possessing favorable pharmacokinetic profiles and biological activities were selected, interacting with 42 BSS-related targets to provide potential synergistic therapeutic actions. Systematic analysis of the constructed networks revealed that these targets such as HMOX1, NOS2, NOS3, HIF1A and PTGS2 were mainly involved in TNF signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway and neurotrophin signaling pathway. The contribution index of every active ingredient also indicated six compounds, including hydroxysafflor yellow A, safflor yellow A, safflor yellow B, Z-ligustilide, ferulic acid, and Z-butylidenephthalide, as the principal components of this herb pair. These results successfully explained the polypharmcological mechanisms underlying the efficiency of Danggui-Honghua for BSS treatment, and also probed into the potential novel therapeutic strategies for BSS in TCM.

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Section: Methodsmentioning

confidence: 99%

Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach

Yue

Xin

Fan

et al. 2017

Sci Rep

113

119

View full text Add to dashboard Cite

show abstract

“…Figure 4 is the flowchart for the communications upon similarity calculation between a CPU host and its GPU device. Some GPU-accelerated similarity calculation algorithms have been reported in the last 1 or 2 years [23,34,35], and our algorithm is similar to the "Integer Fingerprint Algorithm on GPUs," reported by Chao et al [34]. The algorithm pseudocode is described as follows:…”

Section: Structural Similarity Measurementmentioning

confidence: 84%

GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening

Yan

et al. 2012

Mol Divers

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A new algorithm is proposed for accelerating chemical structure similarity search by means of graphic processing unit technology. Experiments demonstrate that the new algorithm is on average more than 120-times faster than the one implemented in conventional central processing unit technology. In order to test the generality of the new algorithm, it has been applied in seven progressive virtual screening experiments on NCI/DTP 60 human cancer cell lines data. The progressive virtual screening results show that the technology can select 10-20% compounds for screening to get 70-80% intrinsic hits for a given chemical library and target.

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“…In the withdrawn drugs-approved drugs network, such withdrawn drugs that contacted with more than 8 approved drugs were selected for cheminformatics studies, where pairwise fingerprint similarity values would be calculated by Tanimoto coefficient measurements [36, 37]. With the definition by Formula (1), a and b represented occurrences of “1” in binary coded strings i and j , respectively, while c was the occurrence of “1” in the same bit of the two ones.…”

Section: Methodsmentioning

confidence: 99%

Predicting the Drug Safety for Traditional Chinese Medicine through a Comparative Analysis of Withdrawn Drugs Using Pharmacological Network

Xue

Zhang

Cai

et al. 2013

Evidence-Based Complementary and Alternative Medicine

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As the major issue to limit the use of drugs, drug safety leads to the attrition or failure in clinical trials of drugs. Therefore, it would be more efficient to minimize therapeutic risks if it could be predicted before large-scale clinical trials. Here, we integrated a network topology analysis with cheminformatics measurements on drug information from the DrugBank database to detect the discrepancies between approved drugs and withdrawn drugs and give drug safety indications. Thus, 47 approved drugs were unfolded with higher similarity measurements to withdrawn ones by the same target and confirmed to be already withdrawn or discontinued in certain countries or regions in subsequent investigations. Accordingly, with the 2D chemical fingerprint similarity calculation as a medium, the method was applied to predict pharmacovigilance for natural products from an in-house traditional Chinese medicine (TCM) database. Among them, Silibinin was highlighted for the high similarity to the withdrawn drug Plicamycin although it was regarded as a promising drug candidate with a lower toxicity in existing reports. In summary, the network approach integrated with cheminformatics could provide drug safety indications effectively, especially for compounds with unknown targets or mechanisms like natural products. It would be helpful for drug safety surveillance in all phases of drug development.

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GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison

Cited by 74 publications

References 22 publications

Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach

Herb pair Danggui-Honghua: mechanisms underlying blood stasis syndrome by system pharmacology approach

GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening

Predicting the Drug Safety for Traditional Chinese Medicine through a Comparative Analysis of Withdrawn Drugs Using Pharmacological Network

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