Computer Science ›› 2017, Vol. 44 ›› Issue (Z11): 552-556.doi: 10.11896/j.issn.1002-137X.2017.11A.117

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Research of Molecular Similarity Algorithm Based on Counting Bloom Filter

WANG Shan, SUN Li, WU Jie, FENG Feng and WANG Hong-wei   

  • Online:2018-12-01 Published:2018-12-01

Abstract: Molecular similarity is an important part of the virtual screening technology,and plays a key role in compu-ter-aid drug design.In the process of 2D Fingerprint similarity assessment,some typical molecular similarity assessment use the Hash function in the process of molecular fingerprint mapping.However,the inherent conflict of Hash function easily reduces the precision of molecular fingerprint mapping.In this paper,a fingerprint mapping method based on counting bloom filter was adopted to effectively reduce the probability of fingerprint space mapping conflict and improved the similarity assessment process.To effectively evaluate molecular similarity,the improved method,which uses a tailored version of DUD (DUD LIB VS.1.0 sets),was validated by comparing with experimental results,using ROCE (Receiver Operating Characteristics Enrichment),AUC (Area Under Curve), awROCE and awAUC value as the evalua-tion standard.Compared with the other original molecular similarity method,the experimental result shows that improved method is still competitive in precision and scaffold hopping potential evaluation standard.

Key words: Molecular similarity,2D Fingerprints,Counting bloom filter,Virtual screening,Computer-aid drug design

[1] NICHOLLS A,MCGAUGHER G B,SHERIDAN R P,et al.Mo-lecular shape and medicinal chemistry:a perspective[J].Journal of Medicinal Chemistry,2010,53(10):3862-3886.
[2] PERRYMAN A L,YU W,WANG X,et al.A virtual screen discovers novel,fragment-sized inhibitors of Mycobacterium tuberculosis InhA[J].Journal of Chemical Information & Modeling,2015,55(3):645-659.
[3] FRANCO P,PORTA N,HOLLIDAY J D,et al.The use of 2D fingerprint methods to support the assessment of structural simi-larity in orphan drug legislation[J].Journal of Cheminforma-tics,2014,6(1):5.
[4] SASTRY G M,ADZHIGIREY M,DAY T,et al.Protein and ligand preparation:parameters,protocols,and influence on virtualscreening enrichments[J].Journal of Computer-aided Molecular Design,2013,27(3):221.
[5] 蔡超前.分子相似性的计算方法研究[D].上海:华东理工大学,2013.
[6] LIU X,JIANG H,LI H.SHAFTS:a hybrid approach for 3D mo-lecular similarity calculation.1.Method and assessment of vir-tual screening[J].Journal of Chemical Information & Modeling,2011,51(9):2372-2385.
[7] VOGT M,STUMPFE D,GEPPERT H,et al.Scaffold Hopping Using Two-Dimensional Fingerprints:True Potential,Black Magic,or a Hopeless Endeavor? Guidelines for Virtual Scree-ning[J].Journal of Medicinal Chemistry,2010,53(15):5707-5715.
[8] LIM H,LEE N,LEE J,et al.Reducing False Positives of a Bloom Filter using Cross-Checking Bloom Filters[J].Applied Mathematics & Information Sciences,2014,8(4):1865-1877.
[9] MELSTED P,PRITCHARD J K.Efficient counting of k-mers in DNA sequences using a bloom filter[J].Bmc Bioinformatics,2011,12(1):333.
[10] RATHGEB C,BREITINGER F,BUSCH C.In Alignment-free cancelable iris biometric templates based on adaptive bloom filters[C]∥2013 International Conference on Biometrics (ICB).IEEE:2013:1-8.
[11] TANG J,FONG A C M,WANG B,et al.A Unified Probabilistic Framework for Name Disambiguation in Digital Library[J].IEEE Transactions on Knowledge & Data Engineering,2012,24(6):975-987.
[12] ECKERT H,BAJORATH J.Molecular similarity analysis invirtual screening:foundations,limitations and novel approaches[J].Drug Discovery Today,2007,12(5-6):225.
[13] CHENG T,LI Q,ZHOU Z,et al.Structure-Based VirtualScreening for Drug Discovery:a Problem-Centric Review[J].Aaps Journal,2012,14(1):133.
[14] VENKATRAMAN V,PREZNUENO V I,M AVIDIS L,et al.Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods[J].Journal of Chemical Information & Modeling,2010,50(12):2079.
[15] JAHN A,HINSELMANN G,FECHNER N,et al.Optimal assignment methods for ligand-based virtual screening[J].Journal of Cheminformatics,2009,1(1):14.
[16] RAMIREZ-MANZANARES A,PEA J,AZPIROZ J M,et al.A hierarchical algorithm for molecular similarity (H-FORMS)[J].Journal of Computational Chemistry,2015,36(19):1456.
[17] HU G,KUANG G,XIAO W,et al.Performance evaluation of 2D fingerprint and 3D shape similarity methods in virtual screening[J].Journal of Chemical Information & Modeling,2012,52(5):1103.
[18] GARDINER E J,HOLLIDAY J D,O’DOWD C,et al.Effectiveness of 2D fingerprints for scaffold hopping[J].Future Medicinal Chemistry,2011,3(4):405.
[19] JAIN A N,NICHOLLS A.Recommendations for evaluation of computational methods[J].Journal of Computer-aided Molecular Design,2008,22(3/4):133.
[20] HESSLER G,BARINGHAUS K H.The scaffold hopping potential of pharmacophores[J].Drug Discovery Today Technologies,2010,7(4):263-269.
[21] VAINIO M J,KOGEJ T,RAUBACHER F,et al.Scaffold Hop-ping by Fragment Replacement[J].Journal of Chemical Information & Modeling,2013,53(7):1825-1835.
[22] CLARK R D,WEBSTER-CLARK D J.Managing bias in ROC curves[J].Journal of computer-aided molecular design,2008,22(3/4):141.

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