Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores

[1]  M. Rarey,et al.  Exploration of Ultralarge Compound Collections for Drug Discovery , 2022, J. Chem. Inf. Model..

[2]  Hans De Winter,et al.  LEADD: Lamarckian evolutionary algorithm for de novo drug design , 2022, Journal of Cheminformatics.

[3]  M. Rarey,et al.  Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces , 2021, J. Chem. Inf. Model..

[4]  Yurii S Moroz,et al.  ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand Discovery , 2020, J. Chem. Inf. Model..

[5]  Matthias Rarey,et al.  Topological Similarity Search in Large Combinatorial Fragment Spaces , 2020, J. Chem. Inf. Model..

[6]  Matthias Rarey,et al.  Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration , 2019, J. Chem. Inf. Model..

[7]  Vidar R. Jensen,et al.  DENOPTIM: Software for Computational de Novo Design of Organic and Inorganic Molecules , 2019, J. Chem. Inf. Model..

[8]  Christian Lemmen,et al.  Comparison of Large Chemical Spaces. , 2019, ACS medicinal chemistry letters.

[9]  Yi Zhao,et al.  Discovery of Potent Inhibitors of 11β-Hydroxysteroid Dehydrogenase Type 1 Using a Novel Growth-Based Protocol of in Silico Screening and Optimization in CONTOUR , 2019, J. Chem. Inf. Model..

[10]  Marcus Gastreich,et al.  The next level in chemical space navigation: going far beyond enumerable compound libraries. , 2019, Drug discovery today.

[11]  Matthias Rarey,et al.  Conformator: A Novel Method for the Generation of Conformer Ensembles , 2019, J. Chem. Inf. Model..

[12]  M. Rarey,et al.  NAOMInext - Synthetically feasible fragment growing in a structure-based design context. , 2019, European journal of medicinal chemistry.

[13]  A. Caflisch,et al.  In silico fragment-based drug design with SEED. , 2018, European journal of medicinal chemistry.

[14]  Matthias Rarey,et al.  FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption , 2016, J. Chem. Inf. Model..

[15]  Eugene I Shakhnovich,et al.  OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. , 2016, Journal of medicinal chemistry.

[16]  Diane Joseph-McCarthy,et al.  Fragment-Based Lead Discovery and Design , 2014, J. Chem. Inf. Model..

[17]  M. Rarey,et al.  Coping with Combinatorial Space in Molecular Design , 2013 .

[18]  Matthias Rarey,et al.  Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces , 2013, J. Chem. Inf. Model..

[19]  Dragos Horvath,et al.  S4MPLE - Sampler For Multiple Protein-Ligand Entities: Simultaneous Docking of Several Entities , 2013, J. Chem. Inf. Model..

[20]  Matthias Rarey,et al.  Searching for Substructures in Fragment Spaces , 2012, J. Chem. Inf. Model..

[21]  Markus Hartenfeller,et al.  DOGS: Reaction-Driven de novo Design of Bioactive Compounds , 2012, PLoS Comput. Biol..

[22]  Matthias Rarey,et al.  NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats , 2011, J. Chem. Inf. Model..

[23]  Matthias Rarey,et al.  De novo design by pharmacophore-based searches in fragment spaces , 2011, J. Comput. Aided Mol. Des..

[24]  Luhua Lai,et al.  LigBuilder 2: A Practical de Novo Drug Design Approach , 2011, J. Chem. Inf. Model..

[25]  Thomas Seidel,et al.  Strategies for 3D pharmacophore-based virtual screening. , 2010, Drug discovery today. Technologies.

[26]  Klaus R. Liedl,et al.  One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space , 2010, J. Chem. Inf. Model..

[27]  Sheng-Yong Yang,et al.  Pharmacophore modeling and applications in drug discovery: challenges and recent advances. , 2010, Drug discovery today.

[28]  Sheng-Yong Yang,et al.  PhDD: a new pharmacophore-based de novo design method of drug-like molecules combined with assessment of synthetic accessibility. , 2010, Journal of molecular graphics & modelling.

[29]  David Rogers,et al.  Extended-Connectivity Fingerprints , 2010, J. Chem. Inf. Model..

[30]  Richard A. Lewis,et al.  Three-dimensional pharmacophore methods in drug discovery. , 2010, Journal of medicinal chemistry.

[31]  C. Murray,et al.  The rise of fragment-based drug discovery. , 2009, Nature chemistry.

[32]  Sebastian G. Rohrer,et al.  Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data , 2009, J. Chem. Inf. Model..

[33]  Matthias Rarey,et al.  On the Art of Compiling and Using 'Drug‐Like' Chemical Fragment Spaces , 2008, ChemMedChem.

[34]  Christian Lemmen,et al.  Similarity searching and scaffold hopping in synthetically accessible combinatorial chemistry spaces. , 2008, Journal of medicinal chemistry.

[35]  Gisbert Schneider,et al.  Flux (2): Comparison of Molecular Mutation and Crossover Operators for Ligand-Based de Novo Design , 2007, J. Chem. Inf. Model..

[36]  Matthias Rarey,et al.  Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations , 2007, J. Chem. Inf. Model..

[37]  Thierry Langer,et al.  Efficient overlay of small organic molecules using 3D pharmacophores , 2007, J. Comput. Aided Mol. Des..

[38]  David E. Shaw,et al.  PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results , 2006, J. Comput. Aided Mol. Des..

[39]  Matthias Rarey,et al.  FlexNovo: Structure‐Based Searching in Large Fragment Spaces , 2006, ChemMedChem.

[40]  Thierry Langer,et al.  Pharmacophores and Pharmacophore Searches: LANGER: PHARMACOPHORES AND PHARMACOPHORE SEARCHES O-BK , 2006 .

[41]  Hugo Kubinyi,et al.  Success Stories of Computer‐Aided Design , 2006 .

[42]  R. Babine,et al.  Crystal Structure of the Catalytic Domain of Human Coagulation Factor XIa in Complex with alpha-Ketothiazole Arginine Derived Ligand , 2006 .

[43]  Ricardo Macarron,et al.  Critical review of the role of HTS in drug discovery. , 2006, Drug discovery today.

[44]  Gisbert Schneider,et al.  Computer-based de novo design of drug-like molecules , 2005, Nature Reviews Drug Discovery.

[45]  Xavier Barril,et al.  Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design. , 2005, Journal of medicinal chemistry.

[46]  Brian K. Shoichet,et al.  Virtual screening of chemical libraries , 2004, Nature.

[47]  Thierry Langer,et al.  Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. , 2003, Current opinion in drug discovery & development.

[48]  Y. Kurogi,et al.  Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. , 2001, Current medicinal chemistry.

[49]  Matthias Rarey,et al.  Similarity searching in large combinatorial chemistry spaces , 2001, J. Comput. Aided Mol. Des..

[50]  A. Good,et al.  3-D pharmacophores in drug discovery. , 2001, Current pharmaceutical design.

[51]  David E. Clark,et al.  Evolutionary Algorithms in Molecular Design: Clark/Evolutionary , 2000 .

[52]  Petra Schneider,et al.  De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks , 2000, J. Comput. Aided Mol. Des..

[53]  Schmid,et al.  "Scaffold-Hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. , 1999, Angewandte Chemie.

[54]  Michael M. Hann,et al.  RECAP-Retrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry , 1998, J. Chem. Inf. Comput. Sci..

[55]  C. Wermuth,et al.  Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998) , 1998 .

[56]  Lothar Thiele,et al.  A Comparison of Selection Schemes Used in Evolutionary Algorithms , 1996, Evolutionary Computation.

[57]  P. Hajduk,et al.  Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.

[58]  Thomas Lengauer,et al.  A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.

[59]  Andrew Smellie,et al.  Identification of Common Functional Configurations Among Molecules , 1996, J. Chem. Inf. Comput. Sci..

[60]  Steven L. Teig,et al.  Chemical Function Queries for 3D Database Search , 1994, J. Chem. Inf. Comput. Sci..

[61]  Arup K. Ghose,et al.  Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics , 1989, J. Chem. Inf. Comput. Sci..

[62]  Gordon M. Crippen,et al.  Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions , 1987, J. Chem. Inf. Comput. Sci..

[63]  W. Kabsch.  A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .

[64]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[65]  D J Rogers,et al.  A Computer Program for Classifying Plants. , 1960, Science.

[66]  Stefan Bietz,et al.  Methoden zur computergestützten Generierung und Aufbereitung von Strukturensembles für Proteinbindetaschen , 2016 .

[67]  Thierry Langer,et al.  Molecule-pharmacophore superpositioning and pattern matching in computational drug design. , 2008, Drug discovery today.

[68]  Thierry Langer,et al.  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters , 2005, J. Chem. Inf. Model..