Markus Lill - Publications

Medicinal Chemistry and Molecular Pharmacology Purdue University, West Lafayette, IN, United States 
Pharmaceutical Chemistry, General Biophysics, Pharmacology, Biochemistry

81 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
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  0.56
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  1
2018 Cassell RJ, Mores KL, Zerfas BL, Mahmoud AH, Lill MA, Trader DJ, van Rijn RM. Rubiscolins are naturally occurring G protein-biased delta opioid receptor peptides. European Neuropsychopharmacology : the Journal of the European College of Neuropsychopharmacology. PMID 30591345 DOI: 10.1016/J.Euroneuro.2018.12.013  0.56
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  1
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  1
2018 Wang Y, Tang S, Harvey KE, Salyer AE, Li TA, Rantz EK, Lill MA, Hockerman GH. Molecular determinants of the differential modulation of Cav1.2 and Cav1.3 by nifedipine and FPL 64176. Molecular Pharmacology. PMID 29980657 DOI: 10.1124/Mol.118.112441  0.32
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  1
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  1
2016 Tabatabaei Ghomi H, Topp EM, Lill MA. Fibpredictor: a computational method for rapid prediction of amyloid fibril structures. Journal of Molecular Modeling. 22: 206. PMID 27502172 DOI: 10.1007/s00894-016-3066-1  1
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  1
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  1
2016 Flowers CR, Costa LJ, Pasquini MC, Le-Rademacher J, Lill M, Shore TB, Vaughan W, Craig M, Freytes CO, Shea TC, Horwitz ME, Fay JW, Mineishi S, Rondelli D, Mason J, et al. Efficacy of Pharmacokinetics-Directed Busulfan, Cyclophosphamide and Etoposide Conditioning and Autologous Stem Cell Transplantation for Lymphoma: Comparison of a Multicenter Phase 2 Study and CIBMTR Outcomes. Biology of Blood and Marrow Transplantation : Journal of the American Society For Blood and Marrow Transplantation. PMID 27040394 DOI: 10.1016/J.Bbmt.2016.03.018  0.32
2015 Moorthy BS, Ghomi HT, Lill MA, Topp EM. Structural transitions and interactions in the early stages of human glucagon amyloid fibrillation. Biophysical Journal. 108: 937-48. PMID 25692598 DOI: 10.1016/j.bpj.2015.01.004  1
2015 Kingsley LJ, Lill MA. Substrate tunnels in enzymes: structure-function relationships and computational methodology. Proteins. 83: 599-611. PMID 25663659 DOI: 10.1002/prot.24772  1
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  0.4
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  1
2014 Thompson JJ, Tabatabaei Ghomi H, Lill MA. Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure. Proteins. 82: 3450-65. PMID 25269778 DOI: 10.1002/prot.24698  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2013 Sadeghi A, Ghasemi SA, Schaefer B, Mohr S, Lill MA, Goedecker S. Metrics for measuring distances in configuration spaces. The Journal of Chemical Physics. 139: 184118. PMID 24320265 DOI: 10.1063/1.4828704  1
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  1
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  1
2013 Morrow ME, Kim MI, Ronau JA, Sheedlo MJ, White RR, Chaney J, Paul LN, Lill MA, Artavanis-Tsakonas K, Das C. Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity. Biochemistry. 52: 3564-78. PMID 23617878 DOI: 10.1021/Bi4003106  1
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  1
2013 Juncosa JI, Hansen M, Bonner LA, Cueva JP, Maglathlin R, McCorvy JD, Marona-Lewicka D, Lill MA, Nichols DE. Extensive rigid analogue design maps the binding conformation of potent N-benzylphenethylamine 5-HT2A serotonin receptor agonist ligands. Acs Chemical Neuroscience. 4: 96-109. PMID 23336049 DOI: 10.1021/Cn3000668  1
2013 Lill MA. Foreword In Silico Drug Discovery and Design. 2-5. DOI: 10.4155/EBO.13.272  1
2013 Wilson GL, Lill MA. Integrating structure- and ligand-based approaches for computer-aided drug design In Silico Drug Discovery and Design. 190-202. DOI: 10.4155/EBO.13.106  1
2013 Lill MA. In silico drug discovery and design In Silico Drug Discovery and Design. 1-223. DOI: 10.4155/9781909453012  1
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  1
2012 Lill Y, Kaserer WA, Newton SM, Lill M, Klebba PE, Ritchie K. Single-molecule study of molecular mobility in the cytoplasm of Escherichia coli. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 021907. PMID 23005785 DOI: 10.1103/Physreve.86.021907  1
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  1
2012 Cueva JP, Chemel BR, Juncosa JI, Lill MA, Watts VJ, Nichols DE. Analogues of doxanthrine reveal differences between the dopamine D1 receptor binding properties of chromanoisoquinolines and hexahydrobenzo[a]phenanthridines. European Journal of Medicinal Chemistry. 48: 97-107. PMID 22204903 DOI: 10.1016/J.Ejmech.2011.11.039  1
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  1
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  1
2012 Wilson GL, Lill MA. Towards a realistic representation in surface-based pseudoreceptor modeling: A PDB-wide analysis of binding pockets Molecular Informatics. 31: 259-271. DOI: 10.1002/minf.201100166  1
2011 Lill MA, Thompson JJ. Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection. Journal of Chemical Information and Modeling. 51: 2680-9. PMID 21870864 DOI: 10.1021/ci200191m  1
2011 Cueva JP, Gallardo-Godoy A, Juncosa JI, Vidi PA, Lill MA, Watts VJ, Nichols DE. Probing the steric space at the floor of the D1 dopamine receptor orthosteric binding domain: 7α-, 7β-, 8α-, and 8β-methyl substituted dihydrexidine analogues. Journal of Medicinal Chemistry. 54: 5508-21. PMID 21714510 DOI: 10.1021/Jm200334C  1
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  1
2011 Lill MA. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry. 50: 6157-69. PMID 21678954 DOI: 10.1021/bi2004558  1
2011 Wilson GL, Lill MA. Integrating structure-based and ligand-based approaches for computational drug design Future Medicinal Chemistry. 3: 735-750. PMID 21554079 DOI: 10.4155/fmc.11.18  1
2011 Bonner LA, Laban U, Chemel BR, Juncosa JI, Lill MA, Watts VJ, Nichols DE. Mapping the catechol binding site in dopamine D₁ receptors: synthesis and evaluation of two parallel series of bicyclic dopamine analogues. Chemmedchem. 6: 1024-40. PMID 21538900 DOI: 10.1002/Cmdc.201100010  1
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  1
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  1
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  1
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  1
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  1
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  0.6
2008 Lill MA. Structure-Based computational approaches to drug metabolism Computational Structural Biology: Methods and Applications. 573-597. DOI: 10.1142/9789812778789_0021  1
2007 Vedani A, Lill MA, Dobler M. Predicting the toxic potential of drugs and chemicals in silico. Altex. 24: 63-6. PMID 19835061  1
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  1
2007 Sharifi N, Hamel E, Lill MA, Risbood P, Kane CT, Hossain MT, Jones A, Dalton JT, Farrar WL. A bifunctional colchicinoid that binds to the androgen receptor. Molecular Cancer Therapeutics. 6: 2328-36. PMID 17699728 DOI: 10.1158/1535-7163.Mct-07-0163  1
2007 Vedani A, Zumstein M, Lill MA, Ernst B. Simulating alpha/beta selectivity at the human thyroid hormone receptor: consensus scoring using multidimensional QSAR. Chemmedchem. 2: 78-87. PMID 17096449 DOI: 10.1002/Cmdc.200600212  1
2006 Lill MA, Vedani A. Combining 4D pharmacophore generation and multidimensional QSAR: modeling ligand binding to the bradykinin B2 receptor. Journal of Chemical Information and Modeling. 46: 2135-45. PMID 16995744 DOI: 10.1021/ci6001944  1
2006 Vedani A, Dobler M, Lill MA. The challenge of predicting drug toxicity in silico. Basic & Clinical Pharmacology & Toxicology. 99: 195-208. PMID 16930291 DOI: 10.1111/j.1742-7843.2006.pto_471.x  1
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  1
2006 Lill Y, Lill MA, Fahrenkrog B, Schwarz-Herion K, Paulillo S, Aebi U, Hecht B. Single hepatitis-B virus core capsid binding to individual nuclear pore complexes in Hela cells. Biophysical Journal. 91: 3123-30. PMID 16877503 DOI: 10.1529/Biophysj.106.087650  1
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  1
2006 Lill MA, Vedani A. Computational Modeling of Receptor-Mediated Toxicity Computational Toxicology: Risk Assessment For Pharmaceutical and Environmental Chemicals. 315-351. DOI: 10.1002/9780470145890.ch12  1
2005 Vedani A, Dobler M, Lill MA. Virtual test kits for predicting harmful effects triggered by drugs and chemicals mediated by specific proteins. Altex. 22: 123-34. PMID 16186988  1
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  1
2005 Lill Y, Martinez KL, Lill MA, Meyer BH, Vogel H, Hecht B. Kinetics of the initial steps of G protein-coupled receptor-mediated cellular signaling revealed by single-molecule imaging. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 1633-40. PMID 16082665 DOI: 10.1002/Cphc.200500111  1
2005 Vedani A, Dobler M, Lill MA. In silico prediction of harmful effects triggered by drugs and chemicals. Toxicology and Applied Pharmacology. 207: 398-407. PMID 16045954 DOI: 10.1016/j.taap.2005.01.055  1
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  1
2005 Lill MA, Dobler M, Vedani A. In silico prediction of receptor-mediated environmental toxic phenomena - Application to endocrine disruption Sar and Qsar in Environmental Research. 16: 149-169. PMID 15844448 DOI: 10.1080/10629360412331319826  1
2005 Vedani A, Dobler M, Dollinger H, Hasselbach KM, Birke F, Lill MA. Novel ligands for the chemokine receptor-3 (CCR3): a receptor-modeling study based on 5D-QSAR. Journal of Medicinal Chemistry. 48: 1515-27. PMID 15743194 DOI: 10.1021/jm040827u  1
2004 Lill MA, Vedani A, Dobler M. Raptor: combining dual-shell representation, induced-fit simulation, and hydrophobicity scoring in receptor modeling: application toward the simulation of structurally diverse ligand sets. Journal of Medicinal Chemistry. 47: 6174-86. PMID 15566288 DOI: 10.1021/jm049687e  1
2004 Olkhova E, Hutter MC, Lill MA, Helms V, Michel H. Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations. Biophysical Journal. 86: 1873-89. PMID 15041635 DOI: 10.1016/S0006-3495(04)74254-X  1
2003 Lill M. [Predictive toxicology: in silico modelling and expert systems]. Altex. 20: 104-5. PMID 12848135  1
2003 Vedani A, Dobler M, Lill MA. Internet laboratory for predicting harmful effects triggered by drugs and chemicals--a progress report. Altex. 20: 85-91. PMID 12764545  1
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  1
2002 Lill MA, Helms V. Proton shuttle in green fluorescent protein studied by dynamic simulations. Proceedings of the National Academy of Sciences of the United States of America. 99: 2778-81. PMID 11880630 DOI: 10.1073/pnas.052520799  1
2001 Lill MA, Helms V. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD) Journal of Chemical Physics. 115: 7993-8005. DOI: 10.1063/1.1407293  1
2001 Lill MA, Helms V. Reaction rates for proton transfer over small barriers and connection to transition state theory Journal of Chemical Physics. 115: 7985-7992. DOI: 10.1063/1.1407292  1
2001 Lill MA, Helms V. Compact parameter set for fast estimation of proton transfer rates Journal of Chemical Physics. 114: 1125-1132. DOI: 10.1063/1.1332993  1
2000 Marten J, Pschiwul T, Lill M, Reinhard PG, Toepffer C, Zwicknagel G. Molecular dynamics simulations of microfields in strongly correlated plasmas Journal De Physique. Iv : Jp. 10. DOI: 10.1051/Jp4:2000596  1
2000 Lill MA, Hutter MC, Helms V. Accounting for environmental effects in ab initio calculations of proton transfer barriers Journal of Physical Chemistry A. 104: 8283-8289.  1
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