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Items: 1 to 20 of 30

1.

An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor.

Liu X, Ye K, van Vlijmen HWT, IJzerman AP, van Westen GJP.

J Cheminform. 2019 May 24;11(1):35. doi: 10.1186/s13321-019-0355-6.

2.

Advances and Challenges in Computational Target Prediction.

Sydow D, Burggraaff L, Szengel A, van Vlijmen HWT, IJzerman AP, van Westen GJP, Volkamer A.

J Chem Inf Model. 2019 May 28;59(5):1728-1742. doi: 10.1021/acs.jcim.8b00832. Epub 2019 Feb 28.

PMID:
30817146
3.

Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling.

Burggraaff L, Oranje P, Gouka R, van der Pijl P, Geldof M, van Vlijmen HWT, IJzerman AP, van Westen GJP.

J Cheminform. 2019 Feb 14;11(1):15. doi: 10.1186/s13321-019-0337-8.

4.

Corrigendum to "Chemical space screening around Phe3 in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings" [Bioorg. Med. Chem. Lett. 28(13) (2018) 2320-2323].

Willemse T, Eiselt E, Hollanders K, Schepens W, van Vlijmen HWT, Chung NN, Blais V, Holleran B, Longpré JM, Schiller PW, Maes BUW, Sarret P, Gendron L, Ballet S.

Bioorg Med Chem Lett. 2018 Nov 1;28(20):3418. doi: 10.1016/j.bmcl.2018.08.023. Epub 2018 Sep 5. No abstract available.

PMID:
30195888
5.

Chemical space screening around Phe3 in opioid peptides: Modulating µ versus δ agonism by Suzuki-Miyaura cross-couplings.

Willemse T, Eiselt E, Hollanders K, Schepens W, van Vlijmen HWT, Chung NN, Blais V, Holleran B, Longpré JM, Schiller PW, Maes BUW, Sarret P, Gendron L, Ballet S.

Bioorg Med Chem Lett. 2018 Jul 15;28(13):2320-2323. doi: 10.1016/j.bmcl.2018.05.015. Epub 2018 May 12. Erratum in: Bioorg Med Chem Lett. 2018 Nov 1;28(20):3418.

6.

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling.

Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP.

J Chem Inf Model. 2017 Dec 26;57(12):2976-2985. doi: 10.1021/acs.jcim.7b00338. Epub 2017 Dec 12.

7.

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set.

Lenselink EB, Ten Dijke N, Bongers B, Papadatos G, van Vlijmen HWT, Kowalczyk W, IJzerman AP, van Westen GJP.

J Cheminform. 2017 Aug 14;9(1):45. doi: 10.1186/s13321-017-0232-0.

8.

Blood-based metabolic signatures in Alzheimer's disease.

de Leeuw FA, Peeters CFW, Kester MI, Harms AC, Struys EA, Hankemeier T, van Vlijmen HWT, van der Lee SJ, van Duijn CM, Scheltens P, Demirkan A, van de Wiel MA, van der Flier WM, Teunissen CE.

Alzheimers Dement (Amst). 2017 Sep 6;8:196-207. doi: 10.1016/j.dadm.2017.07.006. eCollection 2017.

9.

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study.

Keränen H, Pérez-Benito L, Ciordia M, Delgado F, Steinbrecher TB, Oehlrich D, van Vlijmen HW, Trabanco AA, Tresadern G.

J Chem Theory Comput. 2017 Mar 14;13(3):1439-1453. doi: 10.1021/acs.jctc.6b01141. Epub 2017 Feb 3.

PMID:
28103438
10.

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor.

Lenselink EB, Beuming T, van Veen C, Massink A, Sherman W, van Vlijmen HW, IJzerman AP.

J Comput Aided Mol Des. 2016 Oct;30(10):863-874. Epub 2016 Sep 15.

11.

Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening.

Lenselink EB, Jespers W, van Vlijmen HW, IJzerman AP, van Westen GJ.

J Chem Inf Model. 2016 Oct 24;56(10):2053-2060. Epub 2016 Sep 27.

PMID:
27626908
12.

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation.

Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J, Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, Beuming T.

ACS Omega. 2016 Aug 31;1(2):293-304. doi: 10.1021/acsomega.6b00086. Epub 2016 Aug 30.

13.

A community computational challenge to predict the activity of pairs of compounds.

Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R, Chen B, Kim M, Wang T, Heiser LM, Realubit R, Mattioli M, Alvarez MJ, Shen Y; NCI-DREAM Community, Gallahan D, Singer D, Saez-Rodriguez J, Xie Y, Stolovitzky G, Califano A; NCI-DREAM Community.

Nat Biotechnol. 2014 Dec;32(12):1213-22. doi: 10.1038/nbt.3052. Epub 2014 Nov 17.

14.

A community effort to assess and improve drug sensitivity prediction algorithms.

Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G.

Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1.

15.

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP.

J Chem Inf Model. 2014 Jun 23;54(6):1737-46. doi: 10.1021/ci5000455. Epub 2014 Jun 3.

PMID:
24835542
16.

Influence of canonical structure determining residues on antibody affinity and stability.

Clark LA, Demarest SJ, Eldredge J, Jarpe MB, Li Y, Simon K, van Vlijmen HW.

J Struct Biol. 2014 Feb;185(2):223-7. doi: 10.1016/j.jsb.2013.08.009. Epub 2013 Aug 29.

PMID:
23994046
17.

Antibody humanization by redesign of complementarity-determining region residues proximate to the acceptor framework.

Hanf KJ, Arndt JW, Chen LL, Jarpe M, Boriack-Sjodin PA, Li Y, van Vlijmen HW, Pepinsky RB, Simon KJ, Lugovskoy A.

Methods. 2014 Jan 1;65(1):68-76. doi: 10.1016/j.ymeth.2013.06.024. Epub 2013 Jun 28.

PMID:
23816785
18.

Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data.

van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.

PLoS Comput Biol. 2013;9(2):e1002899. doi: 10.1371/journal.pcbi.1002899. Epub 2013 Feb 21.

19.

Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data.

van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A.

J Med Chem. 2012 Aug 23;55(16):7010-20. doi: 10.1021/jm3003069. Epub 2012 Aug 3.

PMID:
22827545
20.

Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development.

van Westen GJ, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, Ijzerman AP, van Vlijmen HW, Bender A.

PLoS One. 2011;6(11):e27518. doi: 10.1371/journal.pone.0027518. Epub 2011 Nov 23.

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