Coping with Combinatorial Space in Molecular Design

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

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

[3]  Jean-Louis Reymond,et al.  Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17 , 2012, J. Chem. Inf. Model..

[4]  Jean-Loup Faulon,et al.  OMG: Open Molecule Generator , 2012, Journal of Cheminformatics.

[5]  Jon Winter,et al.  A System for Encoding and Searching Markush Structures , 2012, J. Chem. Inf. Model..

[6]  J. Reymond,et al.  Exploring chemical space for drug discovery using the chemical universe database. , 2012, ACS chemical neuroscience.

[7]  H. Mei,et al.  Docking and 3D‐QSAR investigations of pyrrolidine derivatives as potent neuraminidase inhibitors , 2012, Chemical biology & drug design.

[8]  Bo Yu,et al.  Size estimation of chemical space: how big is it? , 2012, The Journal of pharmacy and pharmacology.

[9]  Matthias Rarey,et al.  Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT , 2012, J. Chem. Inf. Model..

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

[11]  G. V. Paolini,et al.  Quantifying the chemical beauty of drugs. , 2012, Nature chemistry.

[12]  Jean-Louis Reymond,et al.  Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13 , 2011, J. Chem. Inf. Model..

[13]  Tudor I. Oprea,et al.  Understanding drug‐likeness , 2011 .

[14]  John M. Barnard,et al.  Chemical patent information systems , 2011 .

[15]  Jean-Louis Reymond,et al.  Visualisation and subsets of the chemical universe database GDB-13 for virtual screening , 2011, J. Comput. Aided Mol. Des..

[16]  Markus Hartenfeller,et al.  Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors. , 2011, Future medicinal chemistry.

[17]  Lorenz C. Blum,et al.  Identification of selective norbornane-type aspartate analogue inhibitors of the glutamate transporter 1 (GLT-1) from the chemical universe generated database (GDB). , 2010, Journal of medicinal chemistry.

[18]  Katrin Stierand,et al.  From Structure Diagrams to Visual Chemical Patterns , 2010, J. Chem. Inf. Model..

[19]  D. Bertrand,et al.  Exploring α7-Nicotinic Receptor Ligand Diversity by Scaffold Enumeration from the Chemical Universe Database GDB. , 2010, ACS medicinal chemistry letters.

[20]  Holger Claussen,et al.  KnowledgeSpace - a publicly available virtual chemistry space , 2010, J. Cheminformatics.

[21]  Jóhannes Reynisson,et al.  Known drug space as a metric in exploring the boundaries of drug-like chemical space. , 2009, European journal of medicinal chemistry.

[22]  Jean-Louis Reymond,et al.  3-(aminomethyl)piperazine-2,5-dione as a novel NMDA glycine site inhibitor from the chemical universe database GDB. , 2009, Bioorganic & medicinal chemistry letters.

[23]  Stefan Wetzel,et al.  Interactive exploration of chemical space with Scaffold Hunter. , 2009, Nature chemical biology.

[24]  Lorenz C. Blum,et al.  970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. , 2009, Journal of the American Chemical Society.

[25]  Holger Claussen,et al.  Searching Fragment Spaces with Feature Trees , 2009, J. Chem. Inf. Model..

[26]  José L. Medina-Franco,et al.  Visualization of the Chemical Space in Drug Discovery , 2008 .

[27]  Brian B. Masek,et al.  Virtual Screening for R-Groups, including Predicted pIC50 Contributions, within Large Structural Databases, Using Topomer CoMFA , 2008, J. Chem. Inf. Model..

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

[29]  D. Bertrand,et al.  Discovery of NMDA Glycine Site Inhibitors from the Chemical Universe Database GDB , 2008, ChemMedChem.

[30]  Tudor I. Oprea,et al.  Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings , 2008, J. Chem. Inf. Model..

[31]  Tudor I. Oprea,et al.  Scaffold Topologies. 2. Analysis of Chemical Databases , 2008, J. Chem. Inf. Model..

[32]  Markus Hartenfeller,et al.  Concept of Combinatorial De Novo Design of Drug‐like Molecules by Particle Swarm Optimization , 2008, Chemical biology & drug design.

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

[34]  Gisbert Schneider,et al.  Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity , 2007, J. Chem. Inf. Model..

[35]  Jonathan M. Goodman,et al.  Exploration of the Accessible Chemical Space of Acyclic Alkanes , 2007, J. Chem. Inf. Model..

[36]  Matthias Rarey,et al.  Exploring fragment spaces under multiple physicochemical constraints , 2007, J. Comput. Aided Mol. Des..

[37]  Hiroshi Yamashita,et al.  A Quantitative Approach to the Estimation of Chemical Space from a Given Geometry by the Combination of Atomic Species , 2007 .

[38]  P. Hajduk,et al.  A decade of fragment-based drug design: strategic advances and lessons learned , 2007, Nature Reviews Drug Discovery.

[39]  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..

[40]  Harald Mauser,et al.  Chemical Fragment Spaces for de novo Design , 2007, J. Chem. Inf. Model..

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

[42]  Andreas Reichel,et al.  The role of blood-brain barrier studies in the pharmaceutical industry. , 2006, Current drug metabolism.

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

[44]  Jean-Louis Reymond,et al.  Virtual exploration of the small-molecule chemical universe below 160 Daltons. , 2005, Angewandte Chemie.

[45]  C. Dobson Chemical space and biology , 2004, Nature.

[46]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[47]  H. M. Vinkers,et al.  SYNOPSIS: SYNthesize and OPtimize System in Silico. , 2003, Journal of medicinal chemistry.

[48]  Tudor I. Oprea,et al.  Is There a Difference between Leads and Drugs? A Historical Perspective , 2001, J. Chem. Inf. Comput. Sci..

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

[50]  Patrick Fontana,et al.  Assemble 2.0: a structure generator , 2000 .

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

[52]  Matthias Rarey,et al.  Feature trees: A new molecular similarity measure based on tree matching , 1998, J. Comput. Aided Mol. Des..

[53]  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..

[54]  Mark A. Murcko,et al.  Virtual screening : an overview , 1998 .

[55]  Brendan D. McKay,et al.  Isomorph-Free Exhaustive Generation , 1998, J. Algorithms.

[56]  Pierre Benichou,et al.  Handling Genericity in Chemical Structures Using the Markush Darc Software , 1997, J. Chem. Inf. Comput. Sci..

[57]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .

[58]  Michael F. Lynch,et al.  The Sheffield Generic Structures Project-a Retrospective Review , 1996, J. Chem. Inf. Comput. Sci..

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

[60]  Nikolai S. Zefirov,et al.  Computer Generation of Molecular Structures by the SMOG Program , 1996, J. Chem. Inf. Comput. Sci..

[61]  W. Guida,et al.  The art and practice of structure‐based drug design: A molecular modeling perspective , 1996, Medicinal research reviews.

[62]  Michael F. Lynch,et al.  Computer storage and retrieval of generic chemical structures in patents. 11. Theoretical aspects of the use of structure languages in a retrieval system , 1991, J. Chem. Inf. Comput. Sci..

[63]  William Fisanick,et al.  The Chemical Abstract's Service generic chemical (Markush) structure storage and retrieval capability. 1. Basic concepts , 1990, J. Chem. Inf. Comput. Sci..

[64]  Kimito Funatsu,et al.  Further development of structure generation in the automated structure elucidation system CHEMICS , 1988, J. Chem. Inf. Comput. Sci..

[65]  Woody Sherman,et al.  Computational approaches for fragment-based and de novo design. , 2010, Current topics in medicinal chemistry.

[66]  Matthias Rarey,et al.  LoFT: Similarity-Driven Multiobjective Focused Library Design , 2010, J. Chem. Inf. Model..

[67]  D. Kell,et al.  'Metabolite-likeness' as a criterion in the design and selection of pharmaceutical drug libraries. , 2009, Drug discovery today.

[68]  Brian K. Shoichet,et al.  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..

[69]  R. Cramer,et al.  Topomer CoMFA: a design methodology for rapid lead optimization. , 2003, Journal of medicinal chemistry.

[70]  J M Barnard,et al.  Use of Markush structure analysis techniques for descriptor generation and clustering of large combinatorial libraries. , 2000, Journal of molecular graphics & modelling.

[71]  A. Ghose,et al.  A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. , 1999, Journal of combinatorial chemistry.