Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
暂无分享,去创建一个
[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..