TopologyNet: Topology Based Deep Convolutional and Multi-task Neural Networks for Biomolecular Property Predictions

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2017 Jul 28

PMID 28749969

Citations 102

Authors

Zixuan Cang

Guo-Wei Wei

Affiliations

Soon will be listed here.

Abstract

Availability: weilab.math.msu.edu/TDL/.

Citing Articles

Category-specific topological learning of metal-organic frameworks.

Chen D, Chen C, Wei G J Mater Chem A Mater. 2025; .

PMID: 40027352 PMC: 11869180. DOI: 10.1039/d4ta08877h.

Leveraging Persistent Homology Features for Accurate Defect Formation Energy Predictions via Graph Neural Networks.

Fang Z, Yan Q Chem Mater. 2025; 37(4):1531-1540.

PMID: 40026708 PMC: 11866744. DOI: 10.1021/acs.chemmater.4c03028.

Functionally active modulators targeting the LRRK2 WD40 repeat domain identified by FRASE-bot in CACHE Challenge #1.

Mettu A, Glavatskikh M, Wang X, Lara Ordonez A, Li F, Chau I Chem Sci. 2025; 16(8):3430-3439.

PMID: 39877816 PMC: 11770807. DOI: 10.1039/d4sc07532c.

The algebraic extended atom-type graph-based model for precise ligand-receptor binding affinity prediction.

Mukta F, Rana M, Meyer A, Ellingson S, Nguyen D J Cheminform. 2025; 17(1):10.

PMID: 39844277 PMC: 11756177. DOI: 10.1186/s13321-025-00955-z.

PERSISTENT DIRAC OF PATHS ON DIGRAPHS AND HYPERGRAPHS.

Suwayyid F, Wei G Found Data Sci. 2024; 6(2):124-153.

PMID: 39640928 PMC: 11620167. DOI: 10.3934/fods.2024001.

References

Wang B, Wei G . Object-oriented Persistent Homology. J Comput Phys. 2015; 305:276-299. PMC: 4685963. DOI: 10.1016/j.jcp.2015.10.036. View

Xia K, Zhao Z, Wei G . Multiresolution persistent homology for excessively large biomolecular datasets. J Chem Phys. 2015; 143(13):134103. PMC: 4592433. DOI: 10.1063/1.4931733. View

Lusci A, Pollastri G, Baldi P . Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules. J Chem Inf Model. 2013; 53(7):1563-75. PMC: 3739985. DOI: 10.1021/ci400187y. View

Kucukkal T, Petukh M, Li L, Alexov E . Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Curr Opin Struct Biol. 2015; 32:18-24. PMC: 4511717. DOI: 10.1016/j.sbi.2015.01.003. View

Xia K, Wei G . Persistent homology analysis of protein structure, flexibility, and folding. Int J Numer Method Biomed Eng. 2014; 30(8):814-44. PMC: 4131872. DOI: 10.1002/cnm.2655. View

Verkhivker G, Appelt K, FREER S, Villafranca J . Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995; 8(7):677-91. DOI: 10.1093/protein/8.7.677. View

Quan L, Lv Q, Zhang Y . STRUM: structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics. 2016; 32(19):2936-46. PMC: 5039926. DOI: 10.1093/bioinformatics/btw361. View

Feng X, Xia K, Tong Y, Wei G . Geometric modeling of subcellular structures, organelles, and multiprotein complexes. Int J Numer Method Biomed Eng. 2012; 28(12):1198-223. PMC: 3568658. DOI: 10.1002/cnm.2532. View

Martinez J, Baquero F . Mutation frequencies and antibiotic resistance. Antimicrob Agents Chemother. 2000; 44(7):1771-7. PMC: 89960. DOI: 10.1128/AAC.44.7.1771-1777.2000. View

10.

Xia K, Wei G . Multidimensional persistence in biomolecular data. J Comput Chem. 2015; 36(20):1502-20. PMC: 4485576. DOI: 10.1002/jcc.23953. View

11.

Yang Y, Chen B, Tan G, Vihinen M, Shen B . Structure-based prediction of the effects of a missense variant on protein stability. Amino Acids. 2012; 44(3):847-55. DOI: 10.1007/s00726-012-1407-7. View

12.

Darcy I, Vazquez M . Determining the topology of stable protein-DNA complexes. Biochem Soc Trans. 2013; 41(2):601-5. DOI: 10.1042/BST20130004. View

13.

Gong P, Ye J, Zhang C . Multi-Stage Multi-Task Feature Learning. Adv Neural Inf Process Syst. 2014; 14:2979-3010. PMC: 3889129. View

14.

Zheng Z, Ucisik M, Merz Jr K . The Movable Type Method Applied to Protein-Ligand Binding. J Chem Theory Comput. 2014; 9(12):5526-5538. PMC: 3924725. DOI: 10.1021/ct4005992. View

15.

LeCun Y, Bengio Y, Hinton G . Deep learning. Nature. 2015; 521(7553):436-44. DOI: 10.1038/nature14539. View

16.

Ashtawy H, Mahapatra N . A comparative assessment of ranking accuracies of conventional and machine-learning-based scoring functions for protein-ligand binding affinity prediction. IEEE/ACM Trans Comput Biol Bioinform. 2012; 9(5):1301-13. DOI: 10.1109/TCBB.2012.36. View

17.

Dabaghian Y, Memoli F, FRANK L, Carlsson G . A topological paradigm for hippocampal spatial map formation using persistent homology. PLoS Comput Biol. 2012; 8(8):e1002581. PMC: 3415417. DOI: 10.1371/journal.pcbi.1002581. View

18.

Velec H, Gohlke H, Klebe G . DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem. 2005; 48(20):6296-303. DOI: 10.1021/jm050436v. View

19.

Getov I, Petukh M, Alexov E . SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach. Int J Mol Sci. 2016; 17(4):512. PMC: 4848968. DOI: 10.3390/ijms17040512. View

20.

Cang Z, Wei G . Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction. Int J Numer Method Biomed Eng. 2017; 34(2). DOI: 10.1002/cnm.2914. View