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Markus Lill - Publications

Affiliations: 
Medicinal Chemistry and Molecular Pharmacology Purdue University, West Lafayette, IN, United States 
Area:
Pharmaceutical Chemistry, General Biophysics, Pharmacology, Biochemistry
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Masters MR, Mahmoud AH, Wei Y, Lill MA. Deep Learning Model for Efficient Protein-Ligand Docking with Implicit Side-Chain Flexibility. Journal of Chemical Information and Modeling. 63: 1695-1707. PMID 36916514 DOI: 10.1021/acs.jcim.2c01436  0.409
2020 Ghanbarpour A, Mahmoud AH, Lill MA. Instantaneous generation of protein hydration properties from static structures. Communications Chemistry. 3: 188. PMID 36703451 DOI: 10.1038/s42004-020-00435-5  0.369
2020 Mahmoud AH, Masters MR, Yang Y, Lill MA. Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning. Communications Chemistry. 3: 19. PMID 36703428 DOI: 10.1038/s42004-020-0261-x  0.489
2020 Mahmoud AH, Masters MR, Yang Y, Lill MA. Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning Communications Chemistry. 3. DOI: 10.1038/s42004-020-0261-x  0.33
2019 Bartolowits MD, Gast JM, Hasler AJ, Cirrincione AM, O'Connor RJ, Mahmoud AH, Lill MA, Davisson VJ. Discovery of Inhibitors for Proliferating Cell Nuclear Antigen Using a Computational-Based Linked-Multiple-Fragment Screen. Acs Omega. 4: 15181-15196. PMID 31552364 DOI: 10.1021/acsomega.9b02079  0.335
2019 Mahmoud AH, Yang Y, Lill MA. Improving atom type diversity and sampling in co-solvent simulations using λ-dynamics. Journal of Chemical Theory and Computation. PMID 30933496 DOI: 10.1021/Acs.Jctc.8B00940  0.388
2018 Yang Y, Mahmoud AH, Lill MA. Modeling of halogen-protein interactions in co-solvent molecular dynamics simulations. Journal of Chemical Information and Modeling. PMID 30525593 DOI: 10.1021/Acs.Jcim.8B00806  0.382
2018 Masters MR, Mahmoud AH, Yang Y, Lill MA. Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites. Journal of Chemical Information and Modeling. PMID 30289252 DOI: 10.1021/Acs.Jcim.8B00544  0.372
2018 Yang Y, Abdallah AHA, Lill MA. Calculation of Thermodynamic Properties of Bound Water Molecules. Methods in Molecular Biology (Clifton, N.J.). 1762: 389-402. PMID 29594782 DOI: 10.1007/978-1-4939-7756-7_19  0.442
2017 Yang Y, Hu B, Lill MA. WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization. Methods in Molecular Biology (Clifton, N.J.). 1611: 123-134. PMID 28451976 DOI: 10.1007/978-1-4939-7015-5_10  0.441
2016 Yang Y, Lill MA. Dissecting the Influence of Protein Flexibility on the Location and Thermodynamic Profile of Explicit Water Molecules in Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 27494046 DOI: 10.1021/Acs.Jctc.6B00411  0.446
2016 Kingsley LJ, Esquivel-Rodríguez J, Yang Y, Kihara D, Lill MA. Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations. Journal of Computational Chemistry. PMID 27232548 DOI: 10.1002/Jcc.24412  0.433
2015 Kingsley LJ, Wilson GL, Essex ME, Lill MA. Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates. Pharmaceutical Research. 32: 986-1001. PMID 25208877 DOI: 10.1007/s11095-014-1511-3  0.34
2015 Kingsley LJ, Wilson GL, Essex ME, Lill MA. Combining structure- and ligand-based approaches to improve site of metabolism prediction in CYP2C9 substrates Pharmaceutical Research. 32: 986-1001. DOI: 10.1007/s11095-014-1511-3  0.306
2014 Yang Y, Hu B, Lill MA. Analysis of factors influencing hydration site prediction based on molecular dynamics simulations. Journal of Chemical Information and Modeling. 54: 2987-95. PMID 25252619 DOI: 10.1021/Ci500426Q  0.437
2014 Ghomi HT, Thompson JJ, Lill MA. Are distance-dependent statistical potentials considering three interacting bodies superior to two-body statistical potentials for protein structure prediction? Journal of Bioinformatics and Computational Biology. 12: 1450022. PMID 25212727 DOI: 10.1142/S021972001450022X  0.304
2014 Kingsley LJ, Lill MA. Including ligand-induced protein flexibility into protein tunnel prediction. Journal of Computational Chemistry. 35: 1748-56. PMID 25043499 DOI: 10.1002/jcc.23680  0.375
2014 Pedley AM, Lill MA, Davisson VJ. Flexibility of PCNA-protein interface accommodates differential binding partners. Plos One. 9: e102481. PMID 25036435 DOI: 10.1371/Journal.Pone.0102481  0.322
2014 Kingsley LJ, Lill MA. Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes. Plos One. 9: e99408. PMID 24956479 DOI: 10.1371/journal.pone.0099408  0.399
2014 Hu B, Lill MA. WATsite: hydration site prediction program with PyMOL interface. Journal of Computational Chemistry. 35: 1255-60. PMID 24752524 DOI: 10.1002/jcc.23616  0.329
2014 Hu B, Lill MA. PharmDock: a pharmacophore-based docking program. Journal of Cheminformatics. 6: 14. PMID 24739488 DOI: 10.1186/1758-2946-6-14  0.332
2014 Kingsley LJ, Lill MA. IterTunnel; a method for predicting and evaluating ligand EgressTunnels in proteins with buried active sites Journal of Cheminformatics. 6. DOI: 10.1186/1758-2946-6-S1-P62  0.342
2013 Xu M, Lill MA. Induced fit docking, and the use of QM/MM methods in docking. Drug Discovery Today. Technologies. 10: e411-8. PMID 24050138 DOI: 10.1016/J.Ddtec.2013.02.003  0.583
2013 Hu B, Lill MA. Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking. Journal of Chemical Information and Modeling. 53: 1179-90. PMID 23621564 DOI: 10.1021/ci400143r  0.372
2013 Lill M. Virtual screening in drug design. Methods in Molecular Biology (Clifton, N.J.). 993: 1-12. PMID 23568460 DOI: 10.1007/978-1-62703-342-8_1  0.341
2012 Kortagere S, Lill M, Kerrigan J. Role of computational methods in pharmaceutical sciences. Methods in Molecular Biology (Clifton, N.J.). 929: 21-48. PMID 23007425 DOI: 10.1007/978-1-62703-050-2_3  0.347
2012 Hu B, Lill MA. Protein pharmacophore selection using hydration-site analysis. Journal of Chemical Information and Modeling. 52: 1046-60. PMID 22397751 DOI: 10.1021/ci200620h  0.356
2012 Xu M, Lill MA. Utilizing experimental data for reducing ensemble size in flexible-protein docking. Journal of Chemical Information and Modeling. 52: 187-98. PMID 22146074 DOI: 10.1021/Ci200428T  0.532
2012 Danielson ML, Lill MA. Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring. Proteins. 80: 246-60. PMID 22072600 DOI: 10.1002/Prot.23199  0.688
2011 Danielson ML, Desai PV, Mohutsky MA, Wrighton SA, Lill MA. Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures. European Journal of Medicinal Chemistry. 46: 3953-63. PMID 21703735 DOI: 10.1016/J.Ejmech.2011.05.067  0.689
2011 Lill MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry. 50: 6157-69. PMID 21678954 DOI: 10.1021/bi2004558  0.35
2011 Xu M, Lill MA. Significant enhancement of docking sensitivity using implicit ligand sampling. Journal of Chemical Information and Modeling. 51: 693-706. PMID 21375306 DOI: 10.1021/Ci100457T  0.612
2011 Lill MA, Danielson ML. Computer-aided drug design platform using PyMOL. Journal of Computer-Aided Molecular Design. 25: 13-9. PMID 21053052 DOI: 10.1007/S10822-010-9395-8  0.653
2010 Danielson ML, Lill MA. New computational method for prediction of interacting protein loop regions. Proteins. 78: 1748-59. PMID 20186974 DOI: 10.1002/Prot.22690  0.68
2009 Ekins S, Kortagere S, Iyer M, Reschly EJ, Lill MA, Redinbo MR, Krasowski MD. Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR. Plos Computational Biology. 5: e1000594. PMID 20011107 DOI: 10.1371/Journal.Pcbi.1000594  0.358
2009 Spreafico M, Ernst B, Lill MA, Smiesko M, Vedani A. Mixed-model QSAR at the glucocorticoid receptor: predicting the binding mode and affinity of psychotropic drugs. Chemmedchem. 4: 100-9. PMID 19009570 DOI: 10.1002/Cmdc.200800274  0.323
2008 Jiang Q, Yin X, Lill MA, Danielson ML, Freiser H, Huang J. Long-chain carboxychromanols, metabolites of vitamin E, are potent inhibitors of cyclooxygenases. Proceedings of the National Academy of Sciences of the United States of America. 105: 20464-9. PMID 19074288 DOI: 10.1073/Pnas.0810962106  0.596
2007 Lill MA. Multi-dimensional QSAR in drug discovery. Drug Discovery Today. 12: 1013-7. PMID 18061879 DOI: 10.1016/j.drudis.2007.08.004  0.343
2006 Lill MA, Dobler M, Vedani A. Prediction of small-molecule binding to cytochrome P450 3A4: flexible docking combined with multidimensional QSAR. Chemmedchem. 1: 73-81. PMID 16892339 DOI: 10.1002/cmdc.200500024  0.37
2006 Lill MA. Computational pharmaceutical chemistry - Novel technologies for lead optimization and the prediction of ADMET properties Chimia. 60: 33-36. DOI: 10.2533/000942906777675128  0.406
2005 Lill MA, Winiger F, Vedani A, Ernst B. Impact of induced fit on ligand binding to the androgen receptor: a multidimensional QSAR study to predict endocrine-disrupting effects of environmental chemicals. Journal of Medicinal Chemistry. 48: 5666-74. PMID 16134935 DOI: 10.1021/Jm050403F  0.335
2005 Vedani A, Dobler M, Lill MA. Combining protein modeling and 6D-QSAR. Simulating the binding of structurally diverse ligands to the estrogen receptor. Journal of Medicinal Chemistry. 48: 3700-3. PMID 15916421 DOI: 10.1021/jm050185q  0.307
2003 Dobler M, Lill MA, Vedani A. From crystal structures and their analysis to the in silico prediction of toxic phenomena Helvetica Chimica Acta. 86: 1554-1568. DOI: 10.1002/hlca.200390134  0.309
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