Search Results - "Hert, Jérôme"

mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets by Dalke, Andrew, Hert, Jérôme, Kramer, Christian

“…Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we…”
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The Playbooks of Medicinal Chemistry Design Moves by Awale, Mahendra, Hert, Jérôme, Guasch, Laura, Riniker, Sereina, Kramer, Christian

“…Large databases of biologically relevant molecules, such as ChEMBL, SureChEMBL, or compound collections of pharmaceutical or agrochemical companies, are…”
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Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors by Kuhn, Bernd, Tichý, Michal, Wang, Lingle, Robinson, Shaughnessy, Martin, Rainer E, Kuglstatter, Andreas, Benz, Jörg, Giroud, Maude, Schirmeister, Tanja, Abel, Robert, Diederich, François, Hert, Jérôme

“…Improving the binding affinity of a chemical series by systematically probing one of its exit vectors is a medicinal chemistry activity that can benefit from…”
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Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules by Guba, Wolfgang, Meyder, Agnes, Rarey, Matthias, Hert, Jérôme

“…The Torsion Library contains hundreds of rules for small molecule conformations which have been derived from the Cambridge Structural Database (CSD) and are…”
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Interactive and Versatile Navigation of Structural Databases by Korb, Oliver, Kuhn, Bernd, Hert, Jérôme, Taylor, Neil, Cole, Jason, Groom, Colin, Stahl, Martin

“…We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among…”
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Quantifying the relationships among drug classes by Hert, Jérôme, Keiser, Michael J, Irwin, John J, Oprea, Tudor I, Shoichet, Brian K

“…The similarity of drug targets is typically measured using sequence or structural information. Here, we consider chemo-centric approaches that measure target…”
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New Methods for Ligand-Based Virtual Screening:  Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching by Hert, Jérôme, Willett, Peter, Wilton, David J, Acklin, Pierre, Azzaoui, Kamal, Jacoby, Edgar, Schuffenhauer, Ansgar

“…Similarity searching using a single bioactive reference structure is a well-established technique for accessing chemical structure databases. This paper…”
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CONFECT: Conformations from an Expert Collection of Torsion Patterns by Schärfer, Christin, Schulz-Gasch, Tanja, Hert, Jérôme, Heinzerling, Lennart, Schulz, Benjamin, Inhester, Therese, Stahl, Martin, Rarey, Matthias

“…The generation of sets of low‐energy conformations for a given molecule is a central task in drug design. Herein we present a new conformation generator called…”
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Learning Medicinal Chemistry Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Rules from Cross-Company Matched Molecular Pairs Analysis (MMPA): Miniperspective by Kramer, Christian, Ting, Attilla, Zheng, Hao, Hert, Jérôme, Schindler, Torsten, Stahl, Martin, Robb, Graeme, Crawford, James J, Blaney, Jeff, Montague, Shane, Leach, Andrew G, Dossetter, Al G, Griffen, Ed J

“…The first large scale analysis of in vitro absorption, distribution, metabolism, excretion, and toxicity (ADMET) data shared across multiple major pharma has…”
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Off-target networks derived from ligand set similarity by Keiser, Michael J, Hert, Jérôme

“…Chemically similar drugs often bind biologically diverse protein targets, and proteins with similar sequences or structures do not always recognize the same…”
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A Real-World Perspective on Molecular Design: Miniperspective by Kuhn, Bernd, Guba, Wolfgang, Hert, Jérôme, Banner, David, Bissantz, Caterina, Ceccarelli, Simona, Haap, Wolfgang, Körner, Matthias, Kuglstatter, Andreas, Lerner, Christian, Mattei, Patrizio, Neidhart, Werner, Pinard, Emmanuel, Rudolph, Markus G, Schulz-Gasch, Tanja, Woltering, Thomas, Stahl, Martin

“…We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects,…”
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Enhancing the Effectiveness of Similarity-Based Virtual Screening Using Nearest-Neighbor Information by Hert, Jérôme, Willett, Peter, Wilton, David J, Acklin, Pierre, Azzaoui, Kamal, Jacoby, Edgar, Schuffenhauer, Ansgar

“…We test the hypothesis that fusing the outputs of similarity searches based on a single bioactive reference structure and on its nearest neighbors (of unknown…”
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Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures by Hert, Jérôme, Willett, Peter, Wilton, David J, Acklin, Pierre, Azzaoui, Kamal, Jacoby, Edgar, Schuffenhauer, Ansgar

“…Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews…”
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Predicting new molecular targets for known drugs by Shoichet, Brian K, Roth, Bryan L, Keiser, Michael J, Setola, Vincent, Irwin, John J, Laggner, Christian, Abbas, Atheir I, Hufeisen, Sandra J, Jensen, Niels H, Kuijer, Michael B, Matos, Roberto C, Tran, Thuy B, Whaley, Ryan, Glennon, Richard A, Hert, Jérôme, Thomas, Kelan L. H, Edwards, Douglas D

“…Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many…”
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Identifying mechanism-of-action targets for drugs and probes by Gregori-Puigjané, Elisabet, Setola, Vincent, Hert, Jérôme, Crews, Brenda A, Irwin, John J, Lounkine, Eugen, Marnett, Lawrence, Roth, Bryan L, Shoichet, Brian K

“…Notwithstanding their key roles in therapy and as biological probes, 7% of approved drugs are purported to have no known primary target, and up to 18% lack a…”
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Learning Medicinal Chemistry Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Rules from Cross-Company Matched Molecular Pairs Analysis (MMPA) by Kramer, Christian, Ting, Attilla, Zheng, Hao, Hert, Jérôme, Schindler, Torsten, Stahl, Martin, Robb, Graeme, Crawford, James J, Blaney, Jeff, Montague, Shane, Leach, Andrew G, Dossetter, Al G, Griffen, Ed J

“…The first large scale analysis of in vitro absorption, distribution, metabolism, excretion, and toxicity (ADMET) data shared across multiple major pharma has…”
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Quantifying biogenic bias in screening libraries by Shoichet, Brian K, Hert, Jérôme, Irwin, John J, Laggner, Christian, Keiser, Michael J

“…In lead discovery, libraries of 10 6 molecules are screened for biological activity. Given the over 10 60 drug-like molecules thought possible, such screens…”
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A Real-World Perspective on Molecular Design by Kuhn, Bernd, Guba, Wolfgang, Hert, Jérôme, Banner, David, Bissantz, Caterina, Ceccarelli, Simona, Haap, Wolfgang, Körner, Matthias, Kuglstatter, Andreas, Lerner, Christian, Mattei, Patrizio, Neidhart, Werner, Pinard, Emmanuel, Rudolph, Markus G, Schulz-Gasch, Tanja, Woltering, Thomas, Stahl, Martin

“…We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects,…”
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Can we discover pharmacological promiscuity early in the drug discovery process? by Peters, Jens-Uwe, Hert, Jérôme, Bissantz, Caterina, Hillebrecht, Alexander, Gerebtzoff, Grégori, Bendels, Stefanie, Tillier, Fabien, Migeon, Jacques, Fischer, Holger, Guba, Wolfgang, Kansy, Manfred

“…The term ‘pharmacological promiscuity’ describes the activity of a single compound against multiple targets. When undesired, promiscuity is a major safety…”
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Synthesis, Characterization, and in vivo Evaluation of a Novel Potent Autotaxin-Inhibitor by Hunziker, Daniel, Reinehr, Sabrina, Palmhof, Marina, Wagner, Natalie, Biniasch, Thomas, Stute, Gesa, Mattei, Patrizio, Schmitz, Petra, DiGiorgio, Patrick, Hert, Jérôme, Rudolph, Markus G, Benz, Joerg, Stihle, Martine, Gsell, Bernard, Müller, Stephan, Gasser, Rodolfo, Schonhoven, Nina, Ullmer, Christoph, Joachim, Stephanie C

“…The autotaxin-lysophosphatidic acid (ATX-LPA) signaling pathway plays a role in a variety of autoimmune diseases, such as rheumatoid arthritis or…”
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