Search Results - "Lill, Markus"

Decision Making in Structure-Based Drug Discovery: Visual Inspection of Docking Results by Fischer, André, Smieško, Martin, Sellner, Manuel, Lill, Markus A

“…Molecular docking is a computational method widely used in drug discovery. Due to the inherent inaccuracies of molecular docking, visual inspection of binding…”
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Substrate tunnels in enzymes: Structure-function relationships and computational methodology by Kingsley, Laura J., Lill, Markus A.

“…ABSTRACT In enzymes, the active site is the location where incoming substrates are chemically converted to products. In some enzymes, this site is deeply…”
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Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations by Lill, Markus A

“…Flexibility and dynamics are protein characteristics that are essential for the process of molecular recognition. Conformational changes in the protein that…”
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Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds by Fischer, André, Sellner, Manuel, Neranjan, Santhosh, Smieško, Martin, Lill, Markus A

“…The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious…”
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Computer-aided drug design platform using PyMOL by Lill, Markus A., Danielson, Matthew L.

“…The understanding and optimization of protein-ligand interactions are instrumental to medicinal chemists investigating potential drug candidates. Over the past…”
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WATsite: Hydration site prediction program with PyMOL interface by Hu, Bingjie, Lill, Markus A.

“…Water molecules that mediate protein–ligand interactions or are released from the binding site on ligand binding can contribute both enthalpically and…”
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Deep Learning Model for Efficient Protein–Ligand Docking with Implicit Side-Chain Flexibility by Masters, Matthew R., Mahmoud, Amr H., Wei, Yao, Lill, Markus A.

“…Protein–ligand docking is an essential tool in structure-based drug design with applications ranging from virtual high-throughput screening to pose prediction…”
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Evaluation of Xa inhibitors as potential inhibitors of the SARS-CoV-2 Mpro protease by Papaj, Katarzyna, Spychalska, Patrycja, Kapica, Patryk, Fischer, André, Nowak, Jakub, Bzówka, Maria, Sellner, Manuel, Lill, Markus A, Smieško, Martin, Góra, Artur

“…Based on previous large-scale in silico screening several factor Xa inhibitors were proposed to potentially inhibit SARS-CoV-2 Mpro. In addition to their known…”
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Metrics for measuring distances in configuration spaces by Sadeghi, Ali, Ghasemi, S Alireza, Schaefer, Bastian, Mohr, Stephan, Lill, Markus A, Goedecker, Stefan

“…In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to…”
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Accurate Sampling of Macromolecular Conformations Using Adaptive Deep Learning and Coarse-Grained Representation by Mahmoud, Amr H, Masters, Matthew, Lee, Soo Jung, Lill, Markus A

“…Conformational sampling of protein structures is essential for understanding biochemical functions and for predicting thermodynamic properties such as free…”
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Multi-dimensional QSAR in drug discovery by Lill, Markus A.

“…Quantitative structure–activity relationships (QSAR) is an area of computational research that builds virtual models to predict quantities such as the binding…”
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WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization by Yang, Ying, Hu, Bingjie, Lill, Markus A

“…Water molecules in the binding site of a protein significantly influence protein structure and function, for example, by mediating protein-ligand interactions…”
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PharmDock: a pharmacophore-based docking program by Hu, Bingjie, Lill, Markus A

“…Background Protein-based pharmacophore models are enriched with the information of potential interactions between ligands and the protein target. We have shown…”
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Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR by Ekins, Sean, Kortagere, Sandhya, Iyer, Manisha, Reschly, Erica J, Lill, Markus A, Redinbo, Matthew R, Krasowski, Matthew D

“…Transcriptional regulation of some genes involved in xenobiotic detoxification and apoptosis is performed via the human pregnane X receptor (PXR) which in turn…”
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Conformational Changes of Thyroid Receptors in Response to Antagonists by Fischer, André, Frehner, Gabriela, Lill, Markus A, Smieško, Martin

“…Thyroid hormone receptors (TRs) play a critical role in human development, growth, and metabolism. Antagonists of TRs offer an attractive strategy to treat…”
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Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ‑Dynamics by Mahmoud, Amr H, Yang, Ying, Lill, Markus A

“…Cosolvent molecular dynamics (MD) simulations perform MD simulations of the protein in explicit water mixed with cosolvent molecules that represent functional…”
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Ligand pathways in estrogen-related receptors by Fischer, André, Bardakci, Ferhat, Sellner, Manuel, Lill, Markus A., Smieško, Martin

“…The three subtypes of estrogen-related receptors ERRα, ERRβ, and ERRγ are nuclear receptors mediating metabolic processes in various tissues such as the…”
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Integrating structure-based and ligand-based approaches for computational drug design by Wilson, Gregory L, Lill, Markus A

“…Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the…”
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Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites by Masters, Matthew R, Mahmoud, Amr H, Yang, Ying, Lill, Markus A

“…Molecular dynamics (MD) simulations allow for accurate prediction of the thermodynamic profile of binding-site water molecules critical for protein–ligand…”
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Long-chain carboxychromanols, metabolites of vitamin E, are potent inhibitors of cyclooxygenases by Jiang, Qing, Yin, Xinmin, Lill, Markus A, Danielson, Matthew L, Freiser, Helene, Huang, Jianjie

“…Cyclooxygenase (COX-1/COX-2)-catalyzed eicosanoid formation plays a key role in inflammation-associated diseases. Natural forms of vitamin E are recently shown…”
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