"J Cheminform"[ Journal] - Search Results

Year	Number of Results
2009	22
2010	12
2011	54
2012	39
2013	52
2014	71
2015	78
2016	71
2017	67
2018	68
2019	80
2020	72
2021	100
2022	89
2023	124
2024	45

1

Learning symmetry-aware atom mapping in chemical reactions through deep graph matching.

Astero M, Rousu J. Astero M, et al. J Cheminform. 2024 Apr 22;16(1):46. doi: 10.1186/s13321-024-00841-0. J Cheminform. 2024. PMID: 38650016 Free PMC article.

2

Meta-learning-based Inductive logistic matrix completion for prediction of kinase inhibitors.

Du M, Xie X, Luo J, Li J. Du M, et al. J Cheminform. 2024 Apr 16;16(1):44. doi: 10.1186/s13321-024-00838-9. J Cheminform. 2024. PMID: 38627866 Free article.

3

Classification of substances by health hazard using deep neural networks and molecular electron densities.

Singh S, Zeh G, Freiherr J, Bauer T, Türkmen I, Grasskamp AT. Singh S, et al. J Cheminform. 2024 Apr 16;16(1):45. doi: 10.1186/s13321-024-00835-y. J Cheminform. 2024. PMID: 38627862 Free article.

4

Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents.

Blakey M, Pearman-Kanza S, Frey JG. Blakey M, et al. J Cheminform. 2024 Apr 15;16(1):42. doi: 10.1186/s13321-024-00831-2. J Cheminform. 2024. PMID: 38622746 Free PMC article.

5

PermuteDDS: a permutable feature fusion network for drug-drug synergy prediction.

Zhao X, Xu J, Shui Y, Xu M, Hu J, Liu X, Che K, Wang J, Liu Y. Zhao X, et al. J Cheminform. 2024 Apr 15;16(1):41. doi: 10.1186/s13321-024-00839-8. J Cheminform. 2024. PMID: 38622663 Free PMC article.

6

Mind your prevalence!

Guesné SJJ, Hanser T, Werner S, Boobier S, Scott S. Guesné SJJ, et al. J Cheminform. 2024 Apr 15;16(1):43. doi: 10.1186/s13321-024-00837-w. J Cheminform. 2024. PMID: 38622648 Free PMC article.

7

Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors.

Caba K, Tran-Nguyen VK, Rahman T, Ballester PJ. Caba K, et al. J Cheminform. 2024 Apr 7;16(1):40. doi: 10.1186/s13321-024-00832-1. J Cheminform. 2024. PMID: 38582911 Free PMC article.

8

Using test-time augmentation to investigate explainable AI: inconsistencies between method, model and human intuition.

Hartog PBR, Krüger F, Genheden S, Tetko IV. Hartog PBR, et al. J Cheminform. 2024 Apr 4;16(1):39. doi: 10.1186/s13321-024-00824-1. J Cheminform. 2024. PMID: 38576047 Free PMC article.

9

A general model for predicting enzyme functions based on enzymatic reactions.

Qian W, Wang X, Kang Y, Pan P, Hou T, Hsieh CY. Qian W, et al. J Cheminform. 2024 Mar 31;16(1):38. doi: 10.1186/s13321-024-00827-y. J Cheminform. 2024. PMID: 38556873 Free PMC article.

10

Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices.

Dobbelaere MR, Lengyel I, Stevens CV, Van Geem KM. Dobbelaere MR, et al. J Cheminform. 2024 Mar 29;16(1):37. doi: 10.1186/s13321-024-00834-z. J Cheminform. 2024. PMID: 38553720 Free PMC article.

11

DGet! An open source deuteration calculator for mass spectrometry data.

Lockwood TE, Angeloski A. Lockwood TE, et al. J Cheminform. 2024 Mar 28;16(1):36. doi: 10.1186/s13321-024-00828-x. J Cheminform. 2024. PMID: 38549134 Free PMC article.

12

Effectiveness of molecular fingerprints for exploring the chemical space of natural products.

Boldini D, Ballabio D, Consonni V, Todeschini R, Grisoni F, Sieber SA. Boldini D, et al. J Cheminform. 2024 Mar 25;16(1):35. doi: 10.1186/s13321-024-00830-3. J Cheminform. 2024. PMID: 38528548 Free PMC article.

13

A numerical compass for experiment design in chemical kinetics and molecular property estimation.

Krüger M, Mishra A, Spichtinger P, Pöschl U, Berkemeier T. Krüger M, et al. J Cheminform. 2024 Mar 22;16(1):34. doi: 10.1186/s13321-024-00825-0. J Cheminform. 2024. PMID: 38520014 Free PMC article.

14

Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery.

Shen L, Fang J, Liu L, Yang F, Jenkins JL, Kutchukian PS, Wang H. Shen L, et al. J Cheminform. 2024 Mar 21;16(1):33. doi: 10.1186/s13321-024-00829-w. J Cheminform. 2024. PMID: 38515171 Free PMC article.

15

Advancing material property prediction: using physics-informed machine learning models for viscosity.

Chew AK, Sender M, Kaplan Z, Chandrasekaran A, Chief Elk J, Browning AR, Kwak HS, Halls MD, Afzal MAF. Chew AK, et al. J Cheminform. 2024 Mar 14;16(1):31. doi: 10.1186/s13321-024-00820-5. J Cheminform. 2024. PMID: 38486289 Free PMC article.

16

Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.

Carbery A, Buttenschoen M, Skyner R, von Delft F, Deane CM. Carbery A, et al. J Cheminform. 2024 Mar 14;16(1):32. doi: 10.1186/s13321-024-00821-4. J Cheminform. 2024. PMID: 38486231 Free PMC article.

17

A new workflow for the effective curation of membrane permeability data from open ADME information.

Esaki T, Yonezawa T, Ikeda K. Esaki T, et al. J Cheminform. 2024 Mar 14;16(1):30. doi: 10.1186/s13321-024-00826-z. J Cheminform. 2024. PMID: 38481269 Free PMC article.

18

Automated molecular structure segmentation from documents using ChemSAM.

Tang B, Niu Z, Wang X, Huang J, Ma C, Peng J, Jiang Y, Ge R, Hu H, Lin L, Yang G. Tang B, et al. J Cheminform. 2024 Mar 12;16(1):29. doi: 10.1186/s13321-024-00823-2. J Cheminform. 2024. PMID: 38475916 Free PMC article.

19

Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data.

Jaeger-Honz S, Klein K, Schreiber F. Jaeger-Honz S, et al. J Cheminform. 2024 Mar 12;16(1):28. doi: 10.1186/s13321-024-00822-3. J Cheminform. 2024. PMID: 38475907 Free PMC article.

20

Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy.

Jimenes-Vargas K, Pazos A, Munteanu CR, Perez-Castillo Y, Tejera E. Jimenes-Vargas K, et al. J Cheminform. 2024 Mar 7;16(1):27. doi: 10.1186/s13321-024-00816-1. J Cheminform. 2024. PMID: 38449058 Free PMC article.

21

Small molecule autoencoders: architecture engineering to optimize latent space utility and sustainability.

Oestreich M, Ewert I, Becker M. Oestreich M, et al. J Cheminform. 2024 Mar 5;16(1):26. doi: 10.1186/s13321-024-00817-0. J Cheminform. 2024. PMID: 38444032 Free PMC article.

22

Improving chemical reaction yield prediction using pre-trained graph neural networks.

Han J, Kwon Y, Choi YS, Kang S. Han J, et al. J Cheminform. 2024 Mar 1;16(1):25. doi: 10.1186/s13321-024-00818-z. J Cheminform. 2024. PMID: 38429787 Free PMC article.

23

Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART).

Beyens O, De Winter H. Beyens O, et al. J Cheminform. 2024 Feb 27;16(1):23. doi: 10.1186/s13321-024-00819-y. J Cheminform. 2024. PMID: 38414037 Free PMC article.

24

Prediction of chemical reaction yields with large-scale multi-view pre-training.

Shi R, Yu G, Huo X, Yang Y. Shi R, et al. J Cheminform. 2024 Feb 25;16(1):22. doi: 10.1186/s13321-024-00815-2. J Cheminform. 2024. PMID: 38403627 Free PMC article.

25

"DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases.

Manelfi C, Tazzari V, Lunghini F, Cerchia C, Fava A, Pedretti A, Stouten PFW, Vistoli G, Beccari AR. Manelfi C, et al. J Cheminform. 2024 Feb 23;16(1):21. doi: 10.1186/s13321-024-00813-4. J Cheminform. 2024. PMID: 38395961 Free PMC article.

26

Reinvent 4: Modern AI-driven generative molecule design.

Loeffler HH, He J, Tibo A, Janet JP, Voronov A, Mervin LH, Engkvist O. Loeffler HH, et al. J Cheminform. 2024 Feb 21;16(1):20. doi: 10.1186/s13321-024-00812-5. J Cheminform. 2024. PMID: 38383444 Free PMC article.

27

Free and open-source QSAR-ready workflow for automated standardization of chemical structures in support of QSAR modeling.

Mansouri K, Moreira-Filho JT, Lowe CN, Charest N, Martin T, Tkachenko V, Judson R, Conway M, Kleinstreuer NC, Williams AJ. Mansouri K, et al. J Cheminform. 2024 Feb 20;16(1):19. doi: 10.1186/s13321-024-00814-3. J Cheminform. 2024. PMID: 38378618 Free PMC article.

28

POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor.

Preto AJ, Caniceiro AB, Duarte F, Fernandes H, Ferreira L, Mourão J, Moreira IS. Preto AJ, et al. J Cheminform. 2024 Feb 16;16(1):18. doi: 10.1186/s13321-024-00810-7. J Cheminform. 2024. PMID: 38365724 Free PMC article.

29

Simultaneously improving accuracy and computational cost under parametric constraints in materials property prediction tasks.

Gupta V, Li Y, Peltekian A, Kilic MNT, Liao WK, Choudhary A, Agrawal A. Gupta V, et al. J Cheminform. 2024 Feb 16;16(1):17. doi: 10.1186/s13321-024-00811-6. J Cheminform. 2024. PMID: 38365691 Free PMC article.

30

Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management.

Behr AS, Borgelt H, Kockmann N. Behr AS, et al. J Cheminform. 2024 Feb 7;16(1):16. doi: 10.1186/s13321-024-00807-2. J Cheminform. 2024. PMID: 38326906 Free PMC article.

31

AdductHunter: identifying protein-metal complex adducts in mass spectra.

Long D, Eade L, Sullivan MP, Dost K, Meier-Menches SM, Goldstone DC, Hartinger CG, Wicker JS, Taškova K. Long D, et al. J Cheminform. 2024 Feb 6;16(1):15. doi: 10.1186/s13321-023-00797-7. J Cheminform. 2024. PMID: 38321500 Free PMC article.

32

DLM-DTI: a dual language model for the prediction of drug-target interaction with hint-based learning.

Lee J, Jun DW, Song I, Kim Y. Lee J, et al. J Cheminform. 2024 Feb 1;16(1):14. doi: 10.1186/s13321-024-00808-1. J Cheminform. 2024. PMID: 38297330 Free PMC article.

33

CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm.

Gahlawat A, Singh A, Sandhu H, Garg P. Gahlawat A, et al. J Cheminform. 2024 Jan 30;16(1):12. doi: 10.1186/s13321-024-00803-6. J Cheminform. 2024. PMID: 38291536 Free PMC article.

34

Large-scale comparison of machine learning methods for profiling prediction of kinase inhibitors.

Wu J, Chen Y, Wu J, Zhao D, Huang J, Lin M, Wang L. Wu J, et al. J Cheminform. 2024 Jan 30;16(1):13. doi: 10.1186/s13321-023-00799-5. J Cheminform. 2024. PMID: 38291477 Free PMC article.

35

Enhancing chemical synthesis: a two-stage deep neural network for predicting feasible reaction conditions.

Chen LY, Li YP. Chen LY, et al. J Cheminform. 2024 Jan 24;16(1):11. doi: 10.1186/s13321-024-00805-4. J Cheminform. 2024. PMID: 38268009 Free article.

36

Decrypting orphan GPCR drug discovery via multitask learning.

Huang WC, Lin WT, Hung MS, Lee JC, Tung CW. Huang WC, et al. J Cheminform. 2024 Jan 23;16(1):10. doi: 10.1186/s13321-024-00806-3. J Cheminform. 2024. PMID: 38263092 Free PMC article.

37

MATEO: intermolecular α-amidoalkylation theoretical enantioselectivity optimization. Online tool for selection and design of chiral catalysts and products.

Carracedo-Reboredo P, Aranzamendi E, He S, Arrasate S, Munteanu CR, Fernandez-Lozano C, Sotomayor N, Lete E, González-Díaz H. Carracedo-Reboredo P, et al. J Cheminform. 2024 Jan 23;16(1):9. doi: 10.1186/s13321-024-00802-7. J Cheminform. 2024. PMID: 38254200 Free PMC article.

38

IDSL_MINT: a deep learning framework to predict molecular fingerprints from mass spectra.

Baygi SF, Barupal DK. Baygi SF, et al. J Cheminform. 2024 Jan 18;16(1):8. doi: 10.1186/s13321-024-00804-5. J Cheminform. 2024. PMID: 38238779 Free PMC article.

39

Are new ideas harder to find? A note on incremental research and Journal of Cheminformatics' Scientific Contribution Statement.

Zdrazil B, Guha R, Martinez-Mayorga K, Jeliazkova N. Zdrazil B, et al. J Cheminform. 2024 Jan 15;16(1):6. doi: 10.1186/s13321-023-00798-6. J Cheminform. 2024. PMID: 38221625 Free PMC article. No abstract available.

40

BioisoIdentifier: an online free tool to investigate local structural replacements from PDB.

Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. Zhang T, et al. J Cheminform. 2024 Jan 13;16(1):7. doi: 10.1186/s13321-024-00801-8. J Cheminform. 2024. PMID: 38218937 Free PMC article.

41

Cobdock: an accurate and practical machine learning-based consensus blind docking method.

Ugurlu SY, McDonald D, Lei H, Jones AM, Li S, Tong HY, Butler MS, He S. Ugurlu SY, et al. J Cheminform. 2024 Jan 11;16(1):5. doi: 10.1186/s13321-023-00793-x. J Cheminform. 2024. PMID: 38212855 Free PMC article.

42

DBPP-Predictor: a novel strategy for prediction of chemical drug-likeness based on property profiles.

Gu Y, Wang Y, Zhu K, Li W, Liu G, Tang Y. Gu Y, et al. J Cheminform. 2024 Jan 5;16(1):4. doi: 10.1186/s13321-024-00800-9. J Cheminform. 2024. PMID: 38183072 Free PMC article.

43

InterDILI: interpretable prediction of drug-induced liver injury through permutation feature importance and attention mechanism.

Lee S, Yoo S. Lee S, et al. J Cheminform. 2024 Jan 3;16(1):1. doi: 10.1186/s13321-023-00796-8. J Cheminform. 2024. PMID: 38173043 Free PMC article.

44

Relative molecule self-attention transformer.

Maziarka Ł, Majchrowski D, Danel T, Gaiński P, Tabor J, Podolak I, Morkisz P, Jastrzębski S. Maziarka Ł, et al. J Cheminform. 2024 Jan 3;16(1):3. doi: 10.1186/s13321-023-00789-7. J Cheminform. 2024. PMID: 38173009 Free PMC article.

45

Structure-based, deep-learning models for protein-ligand binding affinity prediction.

Wang DD, Wu W, Wang R. Wang DD, et al. J Cheminform. 2024 Jan 3;16(1):2. doi: 10.1186/s13321-023-00795-9. J Cheminform. 2024. PMID: 38173000 Free PMC article. Review.

46

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations.

Baillif B, Cole J, Giangreco I, McCabe P, Bender A. Baillif B, et al. J Cheminform. 2023 Dec 21;15(1):124. doi: 10.1186/s13321-023-00794-w. J Cheminform. 2023. PMID: 38129933 Free PMC article.

47

A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database.

Vaitkus A, Merkys A, Sander T, Quirós M, Thiessen PA, Bolton EE, Gražulis S. Vaitkus A, et al. J Cheminform. 2023 Dec 19;15(1):123. doi: 10.1186/s13321-023-00780-2. J Cheminform. 2023. PMID: 38115123 Free PMC article.

48

Ilm-NMR-P31: an open-access ³¹P nuclear magnetic resonance database and data-driven prediction of ³¹P NMR shifts.

Hack J, Jordan M, Schmitt A, Raru M, Zorn HS, Seyfarth A, Eulenberger I, Geitner R. Hack J, et al. J Cheminform. 2023 Dec 18;15(1):122. doi: 10.1186/s13321-023-00792-y. J Cheminform. 2023. PMID: 38111059 Free PMC article.

49

Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets.

Rasmussen MH, Duan C, Kulik HJ, Jensen JH. Rasmussen MH, et al. J Cheminform. 2023 Dec 18;15(1):121. doi: 10.1186/s13321-023-00790-0. J Cheminform. 2023. PMID: 38111020 Free PMC article.

50

AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data.

Shimizu Y, Ohta M, Ishida S, Terayama K, Osawa M, Honma T, Ikeda K. Shimizu Y, et al. J Cheminform. 2023 Dec 13;15(1):120. doi: 10.1186/s13321-023-00791-z. J Cheminform. 2023. PMID: 38093324 Free PMC article.

51

SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches.

Landrum GA, Beckers M, Lanini J, Schneider N, Stiefl N, Riniker S. Landrum GA, et al. J Cheminform. 2023 Dec 11;15(1):119. doi: 10.1186/s13321-023-00787-9. J Cheminform. 2023. PMID: 38082357 Free PMC article.

52

HybridGCN for protein solubility prediction with adaptive weighting of multiple features.

Chen L, Wu R, Zhou F, Zhang H, Liu JK. Chen L, et al. J Cheminform. 2023 Dec 8;15(1):118. doi: 10.1186/s13321-023-00788-8. J Cheminform. 2023. PMID: 38066570 Free PMC article.

53

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

Kunnakkattu IR, Choudhary P, Pravda L, Nadzirin N, Smart OS, Yuan Q, Anyango S, Nair S, Varadi M, Velankar S. Kunnakkattu IR, et al. J Cheminform. 2023 Dec 2;15(1):117. doi: 10.1186/s13321-023-00786-w. J Cheminform. 2023. PMID: 38042830 Free PMC article.

54

Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta.

Lehembre E, Giovannini J, Geslin D, Lepailleur A, Lamotte JL, Auber D, Ouali A, Cremilleux B, Zimmermann A, Cuissart B, Bureau R. Lehembre E, et al. J Cheminform. 2023 Nov 29;15(1):116. doi: 10.1186/s13321-023-00782-0. J Cheminform. 2023. PMID: 38031134 Free PMC article.

55

EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances.

Xu HQ, Xiao H, Bu JH, Hong YF, Liu YH, Tao ZY, Ding SF, Xia YT, Wu E, Yan Z, Zhang W, Chen GX, Zhu F, Tao L. Xu HQ, et al. J Cheminform. 2023 Nov 28;15(1):115. doi: 10.1186/s13321-023-00779-9. J Cheminform. 2023. PMID: 38017550 Free PMC article.

56

NMR shift prediction from small data quantities.

Rull H, Fischer M, Kuhn S. Rull H, et al. J Cheminform. 2023 Nov 27;15(1):114. doi: 10.1186/s13321-023-00785-x. J Cheminform. 2023. PMID: 38012793 Free PMC article.

57

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification.

Probst D. Probst D. J Cheminform. 2023 Nov 23;15(1):113. doi: 10.1186/s13321-023-00784-y. J Cheminform. 2023. PMID: 37996942 Free PMC article.

58

On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data.

Handa K, Thomas MC, Kageyama M, Iijima T, Bender A. Handa K, et al. J Cheminform. 2023 Nov 21;15(1):112. doi: 10.1186/s13321-023-00781-1. J Cheminform. 2023. PMID: 37990215 Free PMC article.

59

YoDe-Segmentation: automated noise-free retrieval of molecular structures from scientific publications.

Zhou C, Liu W, Song X, Yang M, Peng X. Zhou C, et al. J Cheminform. 2023 Nov 20;15(1):111. doi: 10.1186/s13321-023-00783-z. J Cheminform. 2023. PMID: 37986007 Free PMC article.

60

BBB-PEP-prediction: improved computational model for identification of blood-brain barrier peptides using blending position relative composition specific features and ensemble modeling.

Naseem A, Alturise F, Alkhalifah T, Khan YD. Naseem A, et al. J Cheminform. 2023 Nov 18;15(1):110. doi: 10.1186/s13321-023-00773-1. J Cheminform. 2023. PMID: 37980534 Free PMC article.

61

HD_BPMDS: a curated binary pattern multitarget dataset of Huntington's disease-targeting agents.

Stefan SM, Pahnke J, Namasivayam V. Stefan SM, et al. J Cheminform. 2023 Nov 17;15(1):109. doi: 10.1186/s13321-023-00775-z. J Cheminform. 2023. PMID: 37978560 Free PMC article.

62

Correction: MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal-organic frameworks utilizing graph convolutional networks.

Jalali M, Wonanke ADD, Wöll C. Jalali M, et al. J Cheminform. 2023 Nov 15;15(1):108. doi: 10.1186/s13321-023-00774-0. J Cheminform. 2023. PMID: 37968708 Free PMC article. No abstract available.

63

Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions.

Domingo-Fernández D, Gadiya Y, Mubeen S, Healey D, Norman BH, Colluru V. Domingo-Fernández D, et al. J Cheminform. 2023 Nov 10;15(1):107. doi: 10.1186/s13321-023-00778-w. J Cheminform. 2023. PMID: 37950325 Free PMC article.

64

Continuous symmetry and chirality measures: approximate algorithms for large molecular structures.

Alon G, Ben-Haim Y, Tuvi-Arad I. Alon G, et al. J Cheminform. 2023 Nov 9;15(1):106. doi: 10.1186/s13321-023-00777-x. J Cheminform. 2023. PMID: 37946281 Free PMC article.

65

Evaluating uncertainty-based active learning for accelerating the generalization of molecular property prediction.

Yin T, Panapitiya G, Coda ED, Saldanha EG. Yin T, et al. J Cheminform. 2023 Nov 8;15(1):105. doi: 10.1186/s13321-023-00753-5. J Cheminform. 2023. PMID: 37941055 Free PMC article.

66

Determining the parent and associated fragment formulae in mass spectrometry via the parent subformula graph.

Li S, Bohman B, Flematti GR, Jayatilaka D. Li S, et al. J Cheminform. 2023 Nov 7;15(1):104. doi: 10.1186/s13321-023-00776-y. J Cheminform. 2023. PMID: 37936244 Free PMC article.

67

DeepSA: a deep-learning driven predictor of compound synthesis accessibility.

Wang S, Wang L, Li F, Bai F. Wang S, et al. J Cheminform. 2023 Nov 2;15(1):103. doi: 10.1186/s13321-023-00771-3. J Cheminform. 2023. PMID: 37919805 Free PMC article.

68

EasyDock: customizable and scalable docking tool.

Minibaeva G, Ivanova A, Polishchuk P. Minibaeva G, et al. J Cheminform. 2023 Nov 1;15(1):102. doi: 10.1186/s13321-023-00772-2. J Cheminform. 2023. PMID: 37915072 Free PMC article.

69

DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning.

Fralish Z, Chen A, Skaluba P, Reker D. Fralish Z, et al. J Cheminform. 2023 Oct 27;15(1):101. doi: 10.1186/s13321-023-00769-x. J Cheminform. 2023. PMID: 37885017 Free PMC article.

70

Art driven by visual representations of chemical space.

Gaytán-Hernández D, Chávez-Hernández AL, López-López E, Miranda-Salas J, Saldívar-González FI, Medina-Franco JL. Gaytán-Hernández D, et al. J Cheminform. 2023 Oct 21;15(1):100. doi: 10.1186/s13321-023-00770-4. J Cheminform. 2023. PMID: 37865794 Free PMC article.

71

Prediction of organic compound aqueous solubility using machine learning: a comparison study of descriptor-based and fingerprints-based models.

Tayyebi A, Alshami AS, Rabiei Z, Yu X, Ismail N, Talukder MJ, Power J. Tayyebi A, et al. J Cheminform. 2023 Oct 18;15(1):99. doi: 10.1186/s13321-023-00752-6. J Cheminform. 2023. PMID: 37853492 Free PMC article.

72

Cheminformatics Microservice: unifying access to open cheminformatics toolkits.

Chandrasekhar V, Sharma N, Schaub J, Steinbeck C, Rajan K. Chandrasekhar V, et al. J Cheminform. 2023 Oct 16;15(1):98. doi: 10.1186/s13321-023-00762-4. J Cheminform. 2023. PMID: 37845745 Free PMC article.

73

Pmf-cpi: assessing drug selectivity with a pretrained multi-functional model for compound-protein interactions.

Song N, Dong R, Pu Y, Wang E, Xu J, Guo F. Song N, et al. J Cheminform. 2023 Oct 14;15(1):97. doi: 10.1186/s13321-023-00767-z. J Cheminform. 2023. PMID: 37838703 Free PMC article.

74

Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs.

Gil-Pichardo A, Sánchez-Ruiz A, Colmenarejo G. Gil-Pichardo A, et al. J Cheminform. 2023 Oct 13;15(1):96. doi: 10.1186/s13321-023-00768-y. J Cheminform. 2023. PMID: 37833792 Free PMC article.

75

Bloom filters for molecules.

Medina J, White AD. Medina J, et al. J Cheminform. 2023 Oct 12;15(1):95. doi: 10.1186/s13321-023-00765-1. J Cheminform. 2023. PMID: 37828615 Free PMC article.

76

MOFGalaxyNet: a social network analysis for predicting guest accessibility in metal-organic frameworks utilizing graph convolutional networks.

Jalali M, Wonanke ADD, Wöll C. Jalali M, et al. J Cheminform. 2023 Oct 11;15(1):94. doi: 10.1186/s13321-023-00764-2. J Cheminform. 2023. PMID: 37821998 Free PMC article.

77

Paths to cheminformatics: Q&A with Nathaniel Charest.

Charest N. Charest N. J Cheminform. 2023 Oct 5;15(1):92. doi: 10.1186/s13321-023-00750-8. J Cheminform. 2023. PMID: 37798806 Free PMC article. No abstract available.

78

Paths to cheminformatics: Q&A with Ann M. Richard.

Richard AM. Richard AM. J Cheminform. 2023 Oct 5;15(1):93. doi: 10.1186/s13321-023-00749-1. J Cheminform. 2023. PMID: 37798636 Free PMC article. No abstract available.

79

ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks.

Hu C, Li S, Yang C, Chen J, Xiong Y, Fan G, Liu H, Hong L. Hu C, et al. J Cheminform. 2023 Oct 4;15(1):91. doi: 10.1186/s13321-023-00766-0. J Cheminform. 2023. PMID: 37794460 Free PMC article.

80

Reliable and accurate prediction of basic pK[Formula: see text] values in nitrogen compounds: the pK[Formula: see text] shift in supramolecular systems as a case study.

Alcázar JJ, Misad Saide AC, Campodónico PR. Alcázar JJ, et al. J Cheminform. 2023 Sep 28;15(1):90. doi: 10.1186/s13321-023-00763-3. J Cheminform. 2023. PMID: 37770903 Free PMC article.

81

A molecule perturbation software library and its application to study the effects of molecular design constraints.

Kerstjens A, De Winter H. Kerstjens A, et al. J Cheminform. 2023 Sep 26;15(1):89. doi: 10.1186/s13321-023-00761-5. J Cheminform. 2023. PMID: 37752561 Free PMC article.

82

Probabilistic generative transformer language models for generative design of molecules.

Wei L, Fu N, Song Y, Wang Q, Hu J. Wei L, et al. J Cheminform. 2023 Sep 25;15(1):88. doi: 10.1186/s13321-023-00759-z. J Cheminform. 2023. PMID: 37749655 Free PMC article.

83

Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors.

Durai P, Lee SJ, Lee JW, Pan CH, Park K. Durai P, et al. J Cheminform. 2023 Sep 23;15(1):86. doi: 10.1186/s13321-023-00760-6. J Cheminform. 2023. PMID: 37742003 Free PMC article.

84

Mass-Suite: a novel open-source python package for high-resolution mass spectrometry data analysis.

Hu X, Mar D, Suzuki N, Zhang B, Peter KT, Beck DAC, Kolodziej EP. Hu X, et al. J Cheminform. 2023 Sep 23;15(1):87. doi: 10.1186/s13321-023-00741-9. J Cheminform. 2023. PMID: 37741995 Free PMC article.

85

Exploring the ability of machine learning-based virtual screening models to identify the functional groups responsible for binding.

Hadfield TE, Scantlebury J, Deane CM. Hadfield TE, et al. J Cheminform. 2023 Sep 19;15(1):84. doi: 10.1186/s13321-023-00755-3. J Cheminform. 2023. PMID: 37726844 Free PMC article.

86

Integrating synthetic accessibility with AI-based generative drug design.

Parrot M, Tajmouati H, da Silva VBR, Atwood BR, Fourcade R, Gaston-Mathé Y, Do Huu N, Perron Q. Parrot M, et al. J Cheminform. 2023 Sep 19;15(1):83. doi: 10.1186/s13321-023-00742-8. J Cheminform. 2023. PMID: 37726842 Free PMC article.

87

Extended study on atomic featurization in graph neural networks for molecular property prediction.

Wojtuch A, Danel T, Podlewska S, Maziarka Ł. Wojtuch A, et al. J Cheminform. 2023 Sep 19;15(1):81. doi: 10.1186/s13321-023-00751-7. J Cheminform. 2023. PMID: 37726841 Free PMC article.

88

School of cheminformatics in Latin America.

Gonzalez-Ponce K, Horta Andrade C, Hunter F, Kirchmair J, Martinez-Mayorga K, Medina-Franco JL, Rarey M, Tropsha A, Varnek A, Zdrazil B. Gonzalez-Ponce K, et al. J Cheminform. 2023 Sep 19;15(1):82. doi: 10.1186/s13321-023-00758-0. J Cheminform. 2023. PMID: 37726809 Free PMC article.

89

Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists.

Secker C, Fackeldey K, Weber M, Ray S, Gorgulla C, Schütte C. Secker C, et al. J Cheminform. 2023 Sep 19;15(1):85. doi: 10.1186/s13321-023-00746-4. J Cheminform. 2023. PMID: 37726792 Free PMC article.

90

rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation.

Baquer G, Sementé L, Ràfols P, Martín-Saiz L, Bookmeyer C, Fernández JA, Correig X, García-Altares M. Baquer G, et al. J Cheminform. 2023 Sep 15;15(1):80. doi: 10.1186/s13321-023-00756-2. J Cheminform. 2023. PMID: 37715285 Free PMC article.

91

pyPept: a python library to generate atomistic 2D and 3D representations of peptides.

Ochoa R, Brown JB, Fox T. Ochoa R, et al. J Cheminform. 2023 Sep 12;15(1):79. doi: 10.1186/s13321-023-00748-2. J Cheminform. 2023. PMID: 37700347 Free PMC article.

92

Patch seriation to visualize data and model parameters.

Lasfar R, Tóth G. Lasfar R, et al. J Cheminform. 2023 Sep 9;15(1):78. doi: 10.1186/s13321-023-00757-1. J Cheminform. 2023. PMID: 37689697 Free PMC article.

93

LOGICS: Learning optimal generative distribution for designing de novo chemical structures.

Bae B, Bae H, Nam H. Bae B, et al. J Cheminform. 2023 Sep 7;15(1):77. doi: 10.1186/s13321-023-00747-3. J Cheminform. 2023. PMID: 37674239 Free PMC article.

94

LogD7.4 prediction enhanced by transferring knowledge from chromatographic retention time, microscopic pKa and logP.

Wang Y, Xiong J, Xiao F, Zhang W, Cheng K, Rao J, Niu B, Tong X, Qu N, Zhang R, Wang D, Chen K, Li X, Zheng M. Wang Y, et al. J Cheminform. 2023 Sep 5;15(1):76. doi: 10.1186/s13321-023-00754-4. J Cheminform. 2023. PMID: 37670374 Free PMC article.

95

Zhang Y, Menke J, He J, Nittinger E, Tyrchan C, Koch O, Zhao H. Zhang Y, et al. J Cheminform. 2023 Aug 30;15(1):75. doi: 10.1186/s13321-023-00744-6. J Cheminform. 2023. PMID: 37649050 Free PMC article.

96

Practical guidelines for the use of gradient boosting for molecular property prediction.

Boldini D, Grisoni F, Kuhn D, Friedrich L, Sieber SA. Boldini D, et al. J Cheminform. 2023 Aug 28;15(1):73. doi: 10.1186/s13321-023-00743-7. J Cheminform. 2023. PMID: 37641120 Free PMC article.

97

3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors.

Gorostiola González M, van den Broek RL, Braun TGM, Chatzopoulou M, Jespers W, IJzerman AP, Heitman LH, van Westen GJP. Gorostiola González M, et al. J Cheminform. 2023 Aug 28;15(1):74. doi: 10.1186/s13321-023-00745-5. J Cheminform. 2023. PMID: 37641107 Free PMC article.

98

A deep learning framework for accurate reaction prediction and its application on high-throughput experimentation data.

Li B, Su S, Zhu C, Lin J, Hu X, Su L, Yu Z, Liao K, Chen H. Li B, et al. J Cheminform. 2023 Aug 11;15(1):72. doi: 10.1186/s13321-023-00732-w. J Cheminform. 2023. PMID: 37568183 Free PMC article.

99

DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data.

Kim HW, Zhang C, Reher R, Wang M, Alexander KL, Nothias LF, Han YK, Shin H, Lee KY, Lee KH, Kim MJ, Dorrestein PC, Gerwick WH, Cottrell GW. Kim HW, et al. J Cheminform. 2023 Aug 7;15(1):71. doi: 10.1186/s13321-023-00738-4. J Cheminform. 2023. PMID: 37550756 Free PMC article.

100

Correction: Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization.

Ucak UV, Ashyrmamatov I, Lee J. Ucak UV, et al. J Cheminform. 2023 Jul 31;15(1):70. doi: 10.1186/s13321-023-00740-w. J Cheminform. 2023. PMID: 37525210 Free PMC article. No abstract available.

101

PyL3dMD: Python LAMMPS 3D molecular descriptors package.

Panwar P, Yang Q, Martini A. Panwar P, et al. J Cheminform. 2023 Jul 28;15(1):69. doi: 10.1186/s13321-023-00737-5. J Cheminform. 2023. PMID: 37507792 Free PMC article.

102

Correction: Reconstruction of lossless molecular representations from fingerprints.

Ucak UV, Ashyrmamatov I, Lee J. Ucak UV, et al. J Cheminform. 2023 Jul 26;15(1):68. doi: 10.1186/s13321-023-00739-3. J Cheminform. 2023. PMID: 37496098 Free PMC article. No abstract available.

103

Explaining compound activity predictions with a substructure-aware loss for graph neural networks.

Amara K, Rodríguez-Pérez R, Jiménez-Luna J. Amara K, et al. J Cheminform. 2023 Jul 25;15(1):67. doi: 10.1186/s13321-023-00733-9. J Cheminform. 2023. PMID: 37491407 Free PMC article.

104

The BinDiscover database: a biology-focused meta-analysis tool for 156,000 GC-TOF MS metabolome samples.

Bremer PL, Wohlgemuth G, Fiehn O. Bremer PL, et al. J Cheminform. 2023 Jul 20;15(1):66. doi: 10.1186/s13321-023-00734-8. J Cheminform. 2023. PMID: 37475020 Free PMC article.

105

PINNED: identifying characteristics of druggable human proteins using an interpretable neural network.

Cunningham M, Pins D, Dezső Z, Torrent M, Vasanthakumar A, Pandey A. Cunningham M, et al. J Cheminform. 2023 Jul 19;15(1):64. doi: 10.1186/s13321-023-00735-7. J Cheminform. 2023. PMID: 37468968 Free PMC article.

106

Force field-inspired transformer network assisted crystal density prediction for energetic materials.

Jin JX, Ren GP, Hu J, Liu Y, Gao Y, Wu KJ, He Y. Jin JX, et al. J Cheminform. 2023 Jul 19;15(1):65. doi: 10.1186/s13321-023-00736-6. J Cheminform. 2023. PMID: 37468954 Free PMC article.

107

TB-IECS: an accurate machine learning-based scoring function for virtual screening.

Zhang X, Shen C, Jiang D, Zhang J, Ye Q, Xu L, Hou T, Pan P, Kang Y. Zhang X, et al. J Cheminform. 2023 Jul 4;15(1):63. doi: 10.1186/s13321-023-00731-x. J Cheminform. 2023. PMID: 37403155 Free PMC article.

108

Improving reproducibility and reusability in the Journal of Cheminformatics.

Hoyt CT, Zdrazil B, Guha R, Jeliazkova N, Martinez-Mayorga K, Nittinger E. Hoyt CT, et al. J Cheminform. 2023 Jun 30;15(1):62. doi: 10.1186/s13321-023-00730-y. J Cheminform. 2023. PMID: 37391855 Free PMC article. No abstract available.

109

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL.

Galgonek J, Vondrášek J. Galgonek J, et al. J Cheminform. 2023 Jun 20;15(1):61. doi: 10.1186/s13321-023-00729-5. J Cheminform. 2023. PMID: 37340506 Free PMC article. Review.

110

ProfhEX: AI-based platform for small molecules liability profiling.

Lunghini F, Fava A, Pisapia V, Sacco F, Iaconis D, Beccari AR. Lunghini F, et al. J Cheminform. 2023 Jun 9;15(1):60. doi: 10.1186/s13321-023-00728-6. J Cheminform. 2023. PMID: 37296454 Free PMC article.

111

RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking.

Li J, Fang L, Lou JG. Li J, et al. J Cheminform. 2023 Jun 8;15(1):58. doi: 10.1186/s13321-023-00727-7. J Cheminform. 2023. PMID: 37291642 Free PMC article.

112

Adaptive language model training for molecular design.

Blanchard AE, Bhowmik D, Fox Z, Gounley J, Glaser J, Akpa BS, Irle S. Blanchard AE, et al. J Cheminform. 2023 Jun 8;15(1):59. doi: 10.1186/s13321-023-00719-7. J Cheminform. 2023. PMID: 37291633 Free PMC article.

113

Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation.

Zhang Z, Wang G, Li R, Ni L, Zhang R, Cheng K, Ren Q, Kong X, Ni S, Tong X, Luo L, Wang D, Lu X, Zheng M, Li X. Zhang Z, et al. J Cheminform. 2023 Jun 7;15(1):57. doi: 10.1186/s13321-023-00726-8. J Cheminform. 2023. PMID: 37287071 Free PMC article.

114

Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data.

Seal S, Yang H, Trapotsi MA, Singh S, Carreras-Puigvert J, Spjuth O, Bender A. Seal S, et al. J Cheminform. 2023 Jun 2;15(1):56. doi: 10.1186/s13321-023-00723-x. J Cheminform. 2023. PMID: 37268960 Free PMC article.

115

Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization.

Ucak UV, Ashyrmamatov I, Lee J. Ucak UV, et al. J Cheminform. 2023 May 29;15(1):55. doi: 10.1186/s13321-023-00725-9. J Cheminform. 2023. PMID: 37248531 Free PMC article.

116

Harnessing Shannon entropy-based descriptors in machine learning models to enhance the prediction accuracy of molecular properties.

Guha R, Velegol D. Guha R, et al. J Cheminform. 2023 May 21;15(1):54. doi: 10.1186/s13321-023-00712-0. J Cheminform. 2023. PMID: 37211605 Free PMC article.

117

Combatting over-specialization bias in growing chemical databases.

Dost K, Pullar-Strecker Z, Brydon L, Zhang K, Hafner J, Riddle PJ, Wicker JS. Dost K, et al. J Cheminform. 2023 May 19;15(1):53. doi: 10.1186/s13321-023-00716-w. J Cheminform. 2023. PMID: 37208694 Free PMC article.

118

UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis.

Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, Mohite OS, Nuhamunada M, Kohlbacher O, Weber T. Kontou EE, et al. J Cheminform. 2023 May 12;15(1):52. doi: 10.1186/s13321-023-00724-w. J Cheminform. 2023. PMID: 37173725 Free PMC article.

119

OWSum: algorithmic odor prediction and insight into structure-odor relationships.

Schicker D, Singh S, Freiherr J, Grasskamp AT. Schicker D, et al. J Cheminform. 2023 May 7;15(1):51. doi: 10.1186/s13321-023-00722-y. J Cheminform. 2023. PMID: 37150811 Free PMC article.

120

DeepAR: a novel deep learning-based hybrid framework for the interpretable prediction of androgen receptor antagonists.

Schaduangrat N, Anuwongcharoen N, Charoenkwan P, Shoombuatong W. Schaduangrat N, et al. J Cheminform. 2023 May 6;15(1):50. doi: 10.1186/s13321-023-00721-z. J Cheminform. 2023. PMID: 37149650 Free PMC article.

121

Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation.

Dutschmann TM, Kinzel L, Ter Laak A, Baumann K. Dutschmann TM, et al. J Cheminform. 2023 Apr 28;15(1):49. doi: 10.1186/s13321-023-00709-9. J Cheminform. 2023. PMID: 37118768 Free PMC article.

122

In-silico target prediction by ensemble chemogenomic model based on multi-scale information of chemical structures and protein sequences.

Yang SQ, Zhang LX, Ge YJ, Zhang JW, Hu JX, Shen CY, Lu AP, Hou TJ, Cao DS. Yang SQ, et al. J Cheminform. 2023 Apr 23;15(1):48. doi: 10.1186/s13321-023-00720-0. J Cheminform. 2023. PMID: 37088813 Free PMC article.

123

Exploring QSAR models for activity-cliff prediction.

Dablander M, Hanser T, Lambiotte R, Morris GM. Dablander M, et al. J Cheminform. 2023 Apr 17;15(1):47. doi: 10.1186/s13321-023-00708-w. J Cheminform. 2023. PMID: 37069675 Free PMC article.

124

Biomedical data analyses facilitated by open cheminformatics workflows.

Nittinger E, Clark A, Gaulton A, Zdrazil B. Nittinger E, et al. J Cheminform. 2023 Apr 17;15(1):46. doi: 10.1186/s13321-023-00718-8. J Cheminform. 2023. PMID: 37069670 Free PMC article. No abstract available.

125

Investigation of chemical structure recognition by encoder-decoder models in learning progress.

Nemoto S, Mizuno T, Kusuhara H. Nemoto S, et al. J Cheminform. 2023 Apr 12;15(1):45. doi: 10.1186/s13321-023-00713-z. J Cheminform. 2023. PMID: 37046349 Free PMC article.

126

Principles and requirements for nanomaterial representations to facilitate machine processing and cooperation with nanoinformatics tools.

Blekos K, Chairetakis K, Lynch I, Marcoulaki E. Blekos K, et al. J Cheminform. 2023 Apr 12;15(1):44. doi: 10.1186/s13321-022-00669-6. J Cheminform. 2023. PMID: 37046286 Free PMC article.

127

MetaRF: attention-based random forest for reaction yield prediction with a few trails.

Chen K, Chen G, Li J, Huang Y, Wang E, Hou T, Heng PA. Chen K, et al. J Cheminform. 2023 Apr 10;15(1):43. doi: 10.1186/s13321-023-00715-x. J Cheminform. 2023. PMID: 37038222 Free PMC article.

128

MolFilterGAN: a progressively augmented generative adversarial network for triaging AI-designed molecules.

Liu X, Zhang W, Tong X, Zhong F, Li Z, Xiong Z, Xiong J, Wu X, Fu Z, Tan X, Liu Z, Zhang S, Jiang H, Li X, Zheng M. Liu X, et al. J Cheminform. 2023 Apr 8;15(1):42. doi: 10.1186/s13321-023-00711-1. J Cheminform. 2023. PMID: 37031191 Free PMC article.

129

LinChemIn: SynGraph-a data model and a toolkit to analyze and compare synthetic routes.

Pasquini M, Stenta M. Pasquini M, et al. J Cheminform. 2023 Apr 1;15(1):41. doi: 10.1186/s13321-023-00714-y. J Cheminform. 2023. PMID: 37005691 Free PMC article.

130

VSFlow: an open-source ligand-based virtual screening tool.

Jung S, Vatheuer H, Czodrowski P. Jung S, et al. J Cheminform. 2023 Mar 31;15(1):40. doi: 10.1186/s13321-023-00703-1. J Cheminform. 2023. PMID: 37004101 Free PMC article.

131

qHTSWaterfall: 3-dimensional visualization software for quantitative high-throughput screening (qHTS) data.

Queme B, Braisted JC, Dranchak P, Inglese J. Queme B, et al. J Cheminform. 2023 Mar 31;15(1):39. doi: 10.1186/s13321-023-00717-9. J Cheminform. 2023. PMID: 37004072 Free PMC article.

132

Deep generative model for drug design from protein target sequence.

Chen Y, Wang Z, Wang L, Wang J, Li P, Cao D, Zeng X, Ye X, Sakurai T. Chen Y, et al. J Cheminform. 2023 Mar 28;15(1):38. doi: 10.1186/s13321-023-00702-2. J Cheminform. 2023. PMID: 36978179 Free PMC article.

133

GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES.

Joeres R, Bojar D, Kalinina OV. Joeres R, et al. J Cheminform. 2023 Mar 23;15(1):37. doi: 10.1186/s13321-023-00704-0. J Cheminform. 2023. PMID: 36959676 Free PMC article.

134

Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence.

Lam J, Lewis RJ, Goodman JM. Lam J, et al. J Cheminform. 2023 Mar 21;15(1):36. doi: 10.1186/s13321-023-00706-y. J Cheminform. 2023. PMID: 36945031 Free PMC article.

135

Chemical rules for optimization of chemical mutagenicity via matched molecular pairs analysis and machine learning methods.

Lou C, Yang H, Deng H, Huang M, Li W, Liu G, Lee PW, Tang Y. Lou C, et al. J Cheminform. 2023 Mar 20;15(1):35. doi: 10.1186/s13321-023-00707-x. J Cheminform. 2023. PMID: 36941726 Free PMC article.

136

PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping.

Bahl A, Ibrahim C, Plate K, Haase A, Dengjel J, Nymark P, Dumit VI. Bahl A, et al. J Cheminform. 2023 Mar 19;15(1):34. doi: 10.1186/s13321-023-00710-2. J Cheminform. 2023. PMID: 36935498 Free PMC article.

137

DFFNDDS: prediction of synergistic drug combinations with dual feature fusion networks.

Xu M, Zhao X, Wang J, Feng W, Wen N, Wang C, Wang J, Liu Y, Zhao L. Xu M, et al. J Cheminform. 2023 Mar 16;15(1):33. doi: 10.1186/s13321-023-00690-3. J Cheminform. 2023. PMID: 36927504 Free PMC article.

138

MAW: the reproducible Metabolome Annotation Workflow for untargeted tandem mass spectrometry.

Zulfiqar M, Gadelha L, Steinbeck C, Sorokina M, Peters K. Zulfiqar M, et al. J Cheminform. 2023 Mar 4;15(1):32. doi: 10.1186/s13321-023-00695-y. J Cheminform. 2023. PMID: 36871033 Free PMC article.

139

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity.

Ammar A, Cavill R, Evelo C, Willighagen E. Ammar A, et al. J Cheminform. 2023 Mar 2;15(1):31. doi: 10.1186/s13321-023-00701-3. J Cheminform. 2023. PMID: 36864534 Free PMC article.

140

Correction: Global reactivity models are impactful in industrial synthesis applications.

Neves P, McClure K, Verhoeven J, Dyubankova N, Nugmanov R, Gedich A, Menon S, Shi Z, Wegner JK. Neves P, et al. J Cheminform. 2023 Mar 2;15(1):30. doi: 10.1186/s13321-023-00705-z. J Cheminform. 2023. PMID: 36864495 Free PMC article. No abstract available.

141

ABT-MPNN: an atom-bond transformer-based message-passing neural network for molecular property prediction.

Liu C, Sun Y, Davis R, Cardona ST, Hu P. Liu C, et al. J Cheminform. 2023 Feb 26;15(1):29. doi: 10.1186/s13321-023-00698-9. J Cheminform. 2023. PMID: 36843022 Free PMC article.

142

Predicting RP-LC retention indices of structurally unknown chemicals from mass spectrometry data.

Boelrijk J, van Herwerden D, Ensing B, Forré P, Samanipour S. Boelrijk J, et al. J Cheminform. 2023 Feb 24;15(1):28. doi: 10.1186/s13321-023-00699-8. J Cheminform. 2023. PMID: 36829215 Free PMC article.

143

Reconstruction of lossless molecular representations from fingerprints.

Ucak UV, Ashyrmamatov I, Lee J. Ucak UV, et al. J Cheminform. 2023 Feb 23;15(1):26. doi: 10.1186/s13321-023-00693-0. J Cheminform. 2023. PMID: 36823647 Free PMC article.

144

Double-head transformer neural network for molecular property prediction.

Song Y, Chen J, Wang W, Chen G, Ma Z. Song Y, et al. J Cheminform. 2023 Feb 23;15(1):27. doi: 10.1186/s13321-023-00700-4. J Cheminform. 2023. PMID: 36823530 Free PMC article.

145

Graph isomorphism-based algorithm for cross-checking chemical and crystallographic descriptions.

Merkys A, Vaitkus A, Grybauskas A, Konovalovas A, Quirós M, Gražulis S. Merkys A, et al. J Cheminform. 2023 Feb 23;15(1):25. doi: 10.1186/s13321-023-00692-1. J Cheminform. 2023. PMID: 36814296 Free PMC article.

146

DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning.

Liu X, Ye K, van Vlijmen HWT, IJzerman AP, van Westen GJP. Liu X, et al. J Cheminform. 2023 Feb 20;15(1):24. doi: 10.1186/s13321-023-00694-z. J Cheminform. 2023. PMID: 36803659 Free PMC article.

147

Notes on molecular fragmentation and parameter settings for a dissipative particle dynamics study of a C₁₀E₄/water mixture with lamellar bilayer formation.

Bänsch F, Steinbeck C, Zielesny A. Bänsch F, et al. J Cheminform. 2023 Feb 19;15(1):23. doi: 10.1186/s13321-023-00697-w. J Cheminform. 2023. PMID: 36803857 Free PMC article.

148

UnCorrupt SMILES: a novel approach to de novo design.

Schoenmaker L, Béquignon OJM, Jespers W, van Westen GJP. Schoenmaker L, et al. J Cheminform. 2023 Feb 14;15(1):22. doi: 10.1186/s13321-023-00696-x. J Cheminform. 2023. PMID: 36788579 Free PMC article.

149

Paths to cheminformatics: Q&A with Phyo Phyo Kyaw Zin.

Zin PPK. Zin PPK. J Cheminform. 2023 Feb 13;15(1):21. doi: 10.1186/s13321-022-00668-7. J Cheminform. 2023. PMID: 36782266 Free PMC article. No abstract available.

150

Global reactivity models are impactful in industrial synthesis applications.

Neves P, McClure K, Verhoeven J, Dyubankova N, Nugmanov R, Gedich A, Menon S, Shi Z, Wegner JK. Neves P, et al. J Cheminform. 2023 Feb 11;15(1):20. doi: 10.1186/s13321-023-00685-0. J Cheminform. 2023. PMID: 36774523 Free PMC article.

151

MDSuite: comprehensive post-processing tool for particle simulations.

Tovey S, Zills F, Torres-Herrador F, Lohrmann C, Brückner M, Holm C. Tovey S, et al. J Cheminform. 2023 Feb 11;15(1):19. doi: 10.1186/s13321-023-00687-y. J Cheminform. 2023. PMID: 36774469 Free PMC article.

152

Efficient virtual high-content screening using a distance-aware transformer model.

Sellner MS, Mahmoud AH, Lill MA. Sellner MS, et al. J Cheminform. 2023 Feb 8;15(1):18. doi: 10.1186/s13321-023-00686-z. J Cheminform. 2023. PMID: 36755346 Free PMC article.

153

How to approach machine learning-based prediction of drug/compound-target interactions.

Atas Guvenilir H, Doğan T. Atas Guvenilir H, et al. J Cheminform. 2023 Feb 6;15(1):16. doi: 10.1186/s13321-023-00689-w. J Cheminform. 2023. PMID: 36747300 Free PMC article.

154

Force field-inspired molecular representation learning for property prediction.

Ren GP, Yin YJ, Wu KJ, He Y. Ren GP, et al. J Cheminform. 2023 Feb 6;15(1):17. doi: 10.1186/s13321-023-00691-2. J Cheminform. 2023. PMID: 36747267 Free PMC article.

155

Two years of explicit CiTO annotations.

Willighagen E. Willighagen E. J Cheminform. 2023 Feb 3;15(1):14. doi: 10.1186/s13321-023-00683-2. J Cheminform. 2023. PMID: 36737837 Free PMC article.

156

A look back at a pilot of the citation typing ontology.

Guha R, Zdrazil B, Jeliazkova N, Martinez-Mayorga K. Guha R, et al. J Cheminform. 2023 Feb 3;15(1):15. doi: 10.1186/s13321-023-00684-1. J Cheminform. 2023. PMID: 36737802 Free PMC article. No abstract available.

157

SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering.

Li M, Kang L, Xiong Y, Wang YG, Fan G, Tan P, Hong L. Li M, et al. J Cheminform. 2023 Feb 3;15(1):12. doi: 10.1186/s13321-023-00688-x. J Cheminform. 2023. PMID: 36737798 Free PMC article.

158

Explainable uncertainty quantifications for deep learning-based molecular property prediction.

Yang CI, Li YP. Yang CI, et al. J Cheminform. 2023 Feb 3;15(1):13. doi: 10.1186/s13321-023-00682-3. J Cheminform. 2023. PMID: 36737786 Free PMC article.

159

Generative model based on junction tree variational autoencoder for HOMO value prediction and molecular optimization.

Kondratyev V, Dryzhakov M, Gimadiev T, Slutskiy D. Kondratyev V, et al. J Cheminform. 2023 Feb 2;15(1):11. doi: 10.1186/s13321-023-00681-4. J Cheminform. 2023. PMID: 36732800 Free PMC article.

160

Development of an open-source software for isomer enumeration.

Rieder SR, Oliveira MP, Riniker S, Hünenberger PH. Rieder SR, et al. J Cheminform. 2023 Jan 22;15(1):10. doi: 10.1186/s13321-022-00677-6. J Cheminform. 2023. PMID: 36683047 Free PMC article.

161

Dimensionally reduced machine learning model for predicting single component octanol-water partition coefficients.

Kenney DH, Paffenroth RC, Timko MT, Teixeira AR. Kenney DH, et al. J Cheminform. 2023 Jan 19;15(1):9. doi: 10.1186/s13321-022-00660-1. J Cheminform. 2023. PMID: 36658606 Free PMC article.

162

COMA: efficient structure-constrained molecular generation using contractive and margin losses.

Choi J, Seo S, Park S. Choi J, et al. J Cheminform. 2023 Jan 19;15(1):8. doi: 10.1186/s13321-023-00679-y. J Cheminform. 2023. PMID: 36658602 Free PMC article.

163

New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application.

Letourneau DR, August DD, Volmer DA. Letourneau DR, et al. J Cheminform. 2023 Jan 18;15(1):7. doi: 10.1186/s13321-023-00680-5. J Cheminform. 2023. PMID: 36653829 Free PMC article.

164

Critical assessment of synthetic accessibility scores in computer-assisted synthesis planning.

Skoraczyński G, Kitlas M, Miasojedow B, Gambin A. Skoraczyński G, et al. J Cheminform. 2023 Jan 14;15(1):6. doi: 10.1186/s13321-023-00678-z. J Cheminform. 2023. PMID: 36641473 Free PMC article.

165

Multimodal data fusion for supervised learning-based identification of USP7 inhibitors: a systematic comparison.

Shen WF, Tang HW, Li JB, Li X, Chen S. Shen WF, et al. J Cheminform. 2023 Jan 11;15(1):5. doi: 10.1186/s13321-022-00675-8. J Cheminform. 2023. PMID: 36631899 Free PMC article.

166

Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity.

Tamura S, Miyao T, Bajorath J. Tamura S, et al. J Cheminform. 2023 Jan 7;15(1):4. doi: 10.1186/s13321-022-00676-7. J Cheminform. 2023. PMID: 36611204 Free PMC article.

167

Papyrus: a large-scale curated dataset aimed at bioactivity predictions.

Béquignon OJM, Bongers BJ, Jespers W, IJzerman AP, van der Water B, van Westen GJP. Béquignon OJM, et al. J Cheminform. 2023 Jan 6;15(1):3. doi: 10.1186/s13321-022-00672-x. J Cheminform. 2023. PMID: 36609528 Free PMC article.

168

XSMILES: interactive visualization for molecules, SMILES and XAI attribution scores.

Heberle H, Zhao L, Schmidt S, Wolf T, Heinrich J. Heberle H, et al. J Cheminform. 2023 Jan 6;15(1):2. doi: 10.1186/s13321-022-00673-w. J Cheminform. 2023. PMID: 36609340 Free PMC article.

169

MORTAR: a rich client application for in silico molecule fragmentation.

Bänsch F, Schaub J, Sevindik B, Behr S, Zander J, Steinbeck C, Zielesny A. Bänsch F, et al. J Cheminform. 2023 Jan 2;15(1):1. doi: 10.1186/s13321-022-00674-9. J Cheminform. 2023. PMID: 36593523 Free PMC article.

170

TCMSID: a simplified integrated database for drug discovery from traditional chinese medicine.

Zhang LX, Dong J, Wei H, Shi SH, Lu AP, Deng GM, Cao DS. Zhang LX, et al. J Cheminform. 2022 Dec 31;14(1):89. doi: 10.1186/s13321-022-00670-z. J Cheminform. 2022. PMID: 36587232 Free PMC article.

171

Investigation of the structure-odor relationship using a Transformer model.

Zheng X, Tomiura Y, Hayashi K. Zheng X, et al. J Cheminform. 2022 Dec 29;14(1):88. doi: 10.1186/s13321-022-00671-y. J Cheminform. 2022. PMID: 36581889 Free PMC article.

172

Visualizing chemical space networks with RDKit and NetworkX.

Scalfani VF, Patel VD, Fernandez AM. Scalfani VF, et al. J Cheminform. 2022 Dec 28;14(1):87. doi: 10.1186/s13321-022-00664-x. J Cheminform. 2022. PMID: 36578091 Free PMC article.

173

Human-in-the-loop assisted de novo molecular design.

Sundin I, Voronov A, Xiao H, Papadopoulos K, Bjerrum EJ, Heinonen M, Patronov A, Kaski S, Engkvist O. Sundin I, et al. J Cheminform. 2022 Dec 28;14(1):86. doi: 10.1186/s13321-022-00667-8. J Cheminform. 2022. PMID: 36578043 Free PMC article.

174

An algorithm to classify homologous series within compound datasets.

Lai A, Schaub J, Steinbeck C, Schymanski EL. Lai A, et al. J Cheminform. 2022 Dec 13;14(1):85. doi: 10.1186/s13321-022-00663-y. J Cheminform. 2022. PMID: 36510332 Free PMC article.

175

ReMODE: a deep learning-based web server for target-specific drug design.

Wang M, Wang J, Weng G, Kang Y, Pan P, Li D, Deng Y, Li H, Hsieh CY, Hou T. Wang M, et al. J Cheminform. 2022 Dec 12;14(1):84. doi: 10.1186/s13321-022-00665-w. J Cheminform. 2022. PMID: 36510307 Free PMC article.

176

Predicting chemical structure using reinforcement learning with a stack-augmented conditional variational autoencoder.

Kim H, Ko S, Kim BJ, Ryu SJ, Ahn J. Kim H, et al. J Cheminform. 2022 Dec 9;14(1):83. doi: 10.1186/s13321-022-00666-9. J Cheminform. 2022. PMID: 36494855 Free PMC article.

177

Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds.

Bajorath J, Chávez-Hernández AL, Duran-Frigola M, Fernández-de Gortari E, Gasteiger J, López-López E, Maggiora GM, Medina-Franco JL, Méndez-Lucio O, Mestres J, Miranda-Quintana RA, Oprea TI, Plisson F, Prieto-Martínez FD, Rodríguez-Pérez R, Rondón-Villarreal P, Saldívar-Gonzalez FI, Sánchez-Cruz N, Valli M. Bajorath J, et al. J Cheminform. 2022 Dec 2;14(1):82. doi: 10.1186/s13321-022-00661-0. J Cheminform. 2022. PMID: 36461094 Free PMC article.

178

MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning.

Lin S, Chen W, Chen G, Zhou S, Wei DQ, Xiong Y. Lin S, et al. J Cheminform. 2022 Nov 15;14(1):81. doi: 10.1186/s13321-022-00659-8. J Cheminform. 2022. PMID: 36380384 Free PMC article.

179

Tuning gradient boosting for imbalanced bioassay modelling with custom loss functions.

Boldini D, Friedrich L, Kuhn D, Sieber SA. Boldini D, et al. J Cheminform. 2022 Nov 10;14(1):80. doi: 10.1186/s13321-022-00657-w. J Cheminform. 2022. PMID: 36357942 Free PMC article.

180

Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK).

Schaub J, Zander J, Zielesny A, Steinbeck C. Schaub J, et al. J Cheminform. 2022 Nov 10;14(1):79. doi: 10.1186/s13321-022-00656-x. J Cheminform. 2022. PMID: 36357931 Free PMC article.

181

Naturally-meaningful and efficient descriptors: machine learning of material properties based on robust one-shot ab initio descriptors.

Tawfik SA, Russo SP. Tawfik SA, et al. J Cheminform. 2022 Nov 8;14(1):78. doi: 10.1186/s13321-022-00658-9. J Cheminform. 2022. PMID: 36348412 Free PMC article.

182

Development of machine learning classifiers to predict compound activity on prostate cancer cell lines.

Bonanni D, Pinzi L, Rastelli G. Bonanni D, et al. J Cheminform. 2022 Nov 8;14(1):77. doi: 10.1186/s13321-022-00647-y. J Cheminform. 2022. PMID: 36348374 Free PMC article.

183

Correction : Random-forest model for drug-target interaction prediction via Kullback-Leibler divergence.

Ahn S, Lee SE, Kim MH. Ahn S, et al. J Cheminform. 2022 Nov 2;14(1):76. doi: 10.1186/s13321-022-00653-0. J Cheminform. 2022. PMID: 36324172 Free PMC article. No abstract available.

184

VGSC-DB: an online database of voltage-gated sodium channels.

Wang G, Yu J, Du H, Shen C, Zhang X, Liu Y, Zhang Y, Cao D, Pan P, Hou T. Wang G, et al. J Cheminform. 2022 Nov 1;14(1):75. doi: 10.1186/s13321-022-00655-y. J Cheminform. 2022. PMID: 36320030 Free PMC article.

185

One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data.

Chiesa L, Kellenberger E. Chiesa L, et al. J Cheminform. 2022 Oct 29;14(1):74. doi: 10.1186/s13321-022-00654-z. J Cheminform. 2022. PMID: 36309734 Free PMC article.

186

DrugTax: package for drug taxonomy identification and explainable feature extraction.

Preto AJ, Correia PC, Moreira IS. Preto AJ, et al. J Cheminform. 2022 Oct 27;14(1):73. doi: 10.1186/s13321-022-00649-w. J Cheminform. 2022. PMID: 36303244 Free PMC article.

187

Implementation of a soft grading system for chemistry in a Moodle plugin.

Plyer L, Marcou G, Perves C, Schurhammer R, Varnek A. Plyer L, et al. J Cheminform. 2022 Oct 26;14(1):72. doi: 10.1186/s13321-022-00645-0. J Cheminform. 2022. PMID: 36284337 Free PMC article.

188

A fingerprints based molecular property prediction method using the BERT model.

Wen N, Liu G, Zhang J, Zhang R, Fu Y, Han X. Wen N, et al. J Cheminform. 2022 Oct 21;14(1):71. doi: 10.1186/s13321-022-00650-3. J Cheminform. 2022. PMID: 36271394 Free PMC article.

189

Scalable training of graph convolutional neural networks for fast and accurate predictions of HOMO-LUMO gap in molecules.

Choi JY, Zhang P, Mehta K, Blanchard A, Lupo Pasini M. Choi JY, et al. J Cheminform. 2022 Oct 17;14(1):70. doi: 10.1186/s13321-022-00652-1. J Cheminform. 2022. PMID: 36253845 Free PMC article.

190

Improving VAE based molecular representations for compound property prediction.

Tevosyan A, Khondkaryan L, Khachatrian H, Tadevosyan G, Apresyan L, Babayan N, Stopper H, Navoyan Z. Tevosyan A, et al. J Cheminform. 2022 Oct 14;14(1):69. doi: 10.1186/s13321-022-00648-x. J Cheminform. 2022. PMID: 36242073 Free PMC article.

191

Random-forest model for drug-target interaction prediction via Kullbeck-Leibler divergence.

Ahn S, Lee SE, Kim MH. Ahn S, et al. J Cheminform. 2022 Oct 3;14(1):67. doi: 10.1186/s13321-022-00644-1. J Cheminform. 2022. PMID: 36192818 Free PMC article.

192

Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.

Thomas M, O'Boyle NM, Bender A, de Graaf C. Thomas M, et al. J Cheminform. 2022 Oct 3;14(1):68. doi: 10.1186/s13321-022-00646-z. J Cheminform. 2022. PMID: 36192789 Free PMC article.

193

TUCAN: A molecular identifier and descriptor applicable to the whole periodic table from hydrogen to oganesson.

Brammer JC, Blanke G, Kellner C, Hoffmann A, Herres-Pawlis S, Schatzschneider U. Brammer JC, et al. J Cheminform. 2022 Sep 28;14(1):66. doi: 10.1186/s13321-022-00640-5. J Cheminform. 2022. PMID: 36171627 Free PMC article.

194

Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator.

Chadi MA, Mousannif H, Aamouche A. Chadi MA, et al. J Cheminform. 2022 Sep 27;14(1):65. doi: 10.1186/s13321-022-00643-2. J Cheminform. 2022. PMID: 36167559 Free PMC article.

195

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts.

Yesiltepe Y, Govind N, Metz TO, Renslow RS. Yesiltepe Y, et al. J Cheminform. 2022 Sep 22;14(1):64. doi: 10.1186/s13321-022-00587-7. J Cheminform. 2022. PMID: 36138446 Free PMC article.

196

What makes a reaction network "chemical"?

Müller S, Flamm C, Stadler PF. Müller S, et al. J Cheminform. 2022 Sep 19;14(1):63. doi: 10.1186/s13321-022-00621-8. J Cheminform. 2022. PMID: 36123755 Free PMC article.

197

Machine learning for identification of silylated derivatives from mass spectra.

Ljoncheva M, Stepišnik T, Kosjek T, Džeroski S. Ljoncheva M, et al. J Cheminform. 2022 Sep 15;14(1):62. doi: 10.1186/s13321-022-00636-1. J Cheminform. 2022. PMID: 36109826 Free PMC article.

198

Review of techniques and models used in optical chemical structure recognition in images and scanned documents.

Musazade F, Jamalova N, Hasanov J. Musazade F, et al. J Cheminform. 2022 Sep 9;14(1):61. doi: 10.1186/s13321-022-00642-3. J Cheminform. 2022. PMID: 36076301 Free PMC article. Review.

199

From theory to experiment: transformer-based generation enables rapid discovery of novel reactions.

Wang X, Yao C, Zhang Y, Yu J, Qiao H, Zhang C, Wu Y, Bai R, Duan H. Wang X, et al. J Cheminform. 2022 Sep 2;14(1):60. doi: 10.1186/s13321-022-00638-z. J Cheminform. 2022. PMID: 36056425 Free PMC article.

200

Robustness under parameter and problem domain alterations of Bayesian optimization methods for chemical reactions.

Khondaker RM, Gow S, Kanza S, Frey JG, Niranjan M. Khondaker RM, et al. J Cheminform. 2022 Sep 1;14(1):59. doi: 10.1186/s13321-022-00641-4. J Cheminform. 2022. PMID: 36050750 Free PMC article.

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