Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

V. M. Lam, D. Rodríguez, T. Zhang, E. J. Koh, J. Carlsson and A. Salahpour

Med. Chem. Commun., 2015, 6, 2216
DOI: 10.1039/C5MD00400D

Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models

Claudio N. Cavasotto and Damián Palomba

Chem. Commun., 2015, 51, 13576
DOI: 10.1039/C5CC05050B

Structural insights into serotonin receptor ligands polypharmacology

Sabina Podlewska, Rafał Kafel, Enza Lacivita, Grzegorz Satała, Albert J. Kooistra, Márton Vass, Chris de Graaf, Marcello Leopoldo, Andrzej J. Bojarski and Stefan Mordalski

European Journal of Medicinal Chemistry, 2018, 151, 797
DOI: 10.1016/j.ejmech.2018.04.010

Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

Anirudh Ranganathan, Leigh A. Stoddart, Stephen J. Hill and Jens Carlsson

J. Med. Chem., 2015, 58, 9578
DOI: 10.1021/acs.jmedchem.5b01120

Unpacking the Pathogen Box—An Open Source Tool for Fighting Neglected Tropical Disease

Clinton G. L. Veale

ChemMedChem, 2019, 14, 386
DOI: 10.1002/cmdc.201800755

PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS

Enade P. Istyastono, Muhammad Radifar, Nunung Yuniarti, Vivitri D. Prasasty and Sudi Mungkasi

J. Chem. Inf. Model., 2020, 60, 3697
DOI: 10.1021/acs.jcim.0c00305

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

Mariama Jaiteh, Ismael Rodríguez-Espigares, Jana Selent, Jens Carlsson and Alexander MacKerell

PLoS Comput Biol, 2020, 16, e1007680
DOI: 10.1371/journal.pcbi.1007680

PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors

Enade P. Istyastono, Nunung Yuniarti, Vivitri D. Prasasty and Sudi Mungkasi

Molecules, 2021, 26, 2452
DOI: 10.3390/molecules26092452

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Jon Kapla, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent, Jens Carlsson and Avner Schlessinger

PLoS Comput Biol, 2021, 17, e1008936
DOI: 10.1371/journal.pcbi.1008936

Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT3A, Histamine H1, and Histamine H4Receptors

Sabine Schultes, Albert J. Kooistra, Henry F. Vischer, Saskia Nijmeijer, Eric E. J. Haaksma, Rob Leurs, Iwan J. P. de Esch and Chris de Graaf

J. Chem. Inf. Model., 2015, 55, 1030
DOI: 10.1021/ci500694c

Development and Testing of Druglike Screening Libraries

Junmei Wang, Yubin Ge and Xiang-Qun Xie

J. Chem. Inf. Model., 2019, 59, 53
DOI: 10.1021/acs.jcim.8b00537

Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening

Stanisław Jastrzębski, Maciej Szymczak, Agnieszka Pocha, Stefan Mordalski, Jacek Tabor, Andrzej J. Bojarski and Sabina Podlewska

J. Chem. Inf. Model., 2020, 60, 4246
DOI: 10.1021/acs.jcim.9b01202

Molecular interaction fingerprint approaches for GPCR drug discovery

Márton Vass, Albert J Kooistra, Tina Ritschel, Rob Leurs, Iwan JP de Esch and Chris de Graaf

Current Opinion in Pharmacology, 2016, 30, 59
DOI: 10.1016/j.coph.2016.07.007

Data of small peptides in SMILES and three-dimensional formats for virtual screening campaigns

Vivitri Dewi Prasasty and Enade Perdana Istyastono

Data in Brief, 2019, 27, 104607
DOI: 10.1016/j.dib.2019.104607

Enigmatic Histamine Receptor H4 for Potential Treatment of Multiple Inflammatory, Autoimmune, and Related Diseases

Pakhuri Mehta, Przemysław Miszta, Przemysław Rzodkiewicz, Olga Michalak, Piotr Krzeczyński and Sławomir Filipek

Life, 2020, 10, 50
DOI: 10.3390/life10040050

Structure-based exploration and pharmacological evaluation of N-substituted piperidin-4-yl-methanamine CXCR4 chemokine receptor antagonists

I. Adlere, S. Sun, A. Zarca, L. Roumen, M. Gozelle, C. Perpiñá Viciano, B. Caspar, M. Arimont, J.P. Bebelman, S.J. Briddon, C. Hoffmann, S.J. Hill, M.J. Smit, H.F. Vischer, M. Wijtmans, C. de Graaf, I.J.P. de Esch and R. Leurs

European Journal of Medicinal Chemistry, 2019, 162, 631
DOI: 10.1016/j.ejmech.2018.10.060

Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study

Albert J. Kooistra, Rob Leurs, Iwan J. P. de Esch and Chris de Graaf

J. Chem. Inf. Model., 2015, 55, 1045
DOI: 10.1021/acs.jcim.5b00066

Discovery of a Novel Highly Selective Histamine H4 Receptor Antagonist for the Treatment of Atopic Dermatitis

Kwangseok Ko, Hye-Jung Kim, Pil-Su Ho, Soon Ok Lee, Ji-Eun Lee, Cho-Rong Min, Yu Chul Kim, Ju-Han Yoon, Eun-Jung Park, Young-Jin Kwon, Jee-Hun Yun, Dong-Oh Yoon, Jung-Sook Kim, Woul-Seong Park, Seung-Su Oh, Yu-Mi Song, Woon-Ki Cho, Kazumi Morikawa, Kyoung-June Lee and Chan-Hee Park

J. Med. Chem., 2018, 61, 2949
DOI: 10.1021/acs.jmedchem.7b01855

Matrix metalloproteinase 9 (MMP9) in wound healing of diabetic foot ulcer: Molecular target and structure-based drug design

Maywan Hariono, Sri H. Yuliani, Enade P. Istyastono, Florentinus D.O. Riswanto and Christophorus F. Adhipandito

Wound Medicine, 2018, 22, 1
DOI: 10.1016/j.wndm.2018.05.003

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

Flavio Ballante, Albert J. Kooistra, Stefanie Kampen, Chris de Graaf and Jens Carlsson

Pharmacological Reviews, 2021, 73, 1698
DOI: 10.1124/pharmrev.120.000246

Molecular Modeling of Histamine Receptors—Recent Advances in Drug Discovery

Pakhuri Mehta, Przemysław Miszta and Sławomir Filipek

Molecules, 2021, 26, 1778
DOI: 10.3390/molecules26061778