Ultrafast de novo docking combining pharmacophores and combinatorics

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

[2]  Didier Rognan,et al.  Design of small-sized libraries by combinatorial assembly of linkers and functional groups to a given scaffold: application to the structure-based optimization of a phosphodiesterase 4 inhibitor. , 2005, Journal of medicinal chemistry.

[3]  Denis Khachko,et al.  A very large diversity space of synthetically accessible compounds for use with drug design programs , 2005, J. Comput. Aided Mol. Des..

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

[5]  A. Hopkins,et al.  Navigating chemical space for biology and medicine , 2004, Nature.

[6]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[7]  Shaomeng Wang,et al.  An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes , 2004, J. Chem. Inf. Model..

[8]  Jie Luo,et al.  Retrieval of Crystallographically-Derived Molecular Geometry Information , 2004, J. Chem. Inf. Model..

[9]  S. Mallik,et al.  Protein surface-assisted enhancement in the binding affinity of an inhibitor for recombinant human carbonic anhydrase-II. , 2004, Journal of the American Chemical Society.

[10]  Alexander D. MacKerell,et al.  Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. , 2004, Journal of medicinal chemistry.

[11]  Gerhard Klebe,et al.  Virtual screening for inhibitors of human aldose reductase , 2004, Proteins.

[12]  J. Wendoloski,et al.  Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening. , 2004, Journal of medicinal chemistry.

[13]  M. Rarey Protein–Ligand Docking in Drug Design , 2004 .

[14]  Jordi Mestres,et al.  Guided docking approaches to structure-based design and screening. , 2004, Current topics in medicinal chemistry.

[15]  Sally A. Hindle,et al.  The FlexX database docking environment--rational extraction of receptor based pharmacophores. , 2004, Current drug discovery technologies.

[16]  R. Kisliuk Deaza analogs of folic acid as antitumor agents. , 2003, Current pharmaceutical design.

[17]  Renxiao Wang,et al.  Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.

[18]  A. Rosowsky,et al.  Further studies on the interaction of nonpolyglutamatable aminopterin analogs with dihydrofolate reductase and the reduced folate carrier as determinants of in vitro antitumor activity. , 2003, Biochemical pharmacology.

[19]  Wolfgang Jahnke,et al.  Second-site NMR screening and linker design. , 2003, Current topics in medicinal chemistry.

[20]  Alexander D. MacKerell,et al.  Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening , 2003, J. Chem. Inf. Comput. Sci..

[21]  J. Irwin,et al.  Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.

[22]  F. Allen The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[23]  Joel E. Wright,et al.  Synthesis and in vitro antitumor activity of new deaza analogues of the nonpolyglutamatable antifolate Nα-(4-amino-4-deoxypteroyl)-Nδ-hemiphthaloyl-l-ornithine (PT523) , 2002 .

[24]  Thomas Lengauer,et al.  Flexible docking under pharmacophore type constraints , 2002, J. Comput. Aided Mol. Des..

[25]  Thomas Lengauer,et al.  Bioinformatics ‐ From Genomes to Drugs , 2001 .

[26]  Irwin D. Kuntz,et al.  A genetic algorithm for structure-based de novo design , 2001, J. Comput. Aided Mol. Des..

[27]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

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

[29]  M Rarey,et al.  Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.

[30]  P. Seeburg,et al.  Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. , 2000, Science.

[31]  A. Rosowsky,et al.  Efficient utilization of the reduced folate carrier in CCRF-CEM human leukemic lymphoblasts by the potent antifolate N(alpha)-(4-amino-4-deoxypteroyl)-N(delta)-hemiphthaloyl-L- ornithine (PT523) and its B-ring analogues. , 2000, Biochemical pharmacology.

[32]  A. Rosowsky,et al.  The effect of side-chain, para-aminobenzoyl region, and B-ring modifications on dihydrofolate reductase binding, influx via the reduced folate carrier, and cytotoxicity of the potent nonpolyglutamatable antifolate N(alpha)-(4-amino-4-deoxypteroyl)-N(delta)-hemiphthaloyl-L- ornithine. , 2000, Pharmacology & therapeutics.

[33]  G. Klebe,et al.  Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.

[34]  A R Leach,et al.  Synergy between combinatorial chemistry and de novo design. , 2000, Journal of molecular graphics & modelling.

[35]  Osman F. Güner,et al.  Pharmacophore perception, development, and use in drug design , 2000 .

[36]  Thomas Lengauer,et al.  Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.

[37]  P. Hajduk,et al.  Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. , 1999, Journal of medicinal chemistry.

[38]  A. Rosowsky PT523 and other aminopterin analogs with a hemiphthaloyl-L-ornithine side chain: exceptionally tight-binding inhibitors of dihydrofolate reductase which are transported by the reduced folate carrier but cannot form polyglutamates. , 1999, Current medicinal chemistry.

[39]  Jeremy R. H. Tame,et al.  Scoring functions: A view from the bench , 1999, J. Comput. Aided Mol. Des..

[40]  Thomas Lengauer,et al.  Docking of hydrophobic ligands with interaction-based matching algorithms , 1999, German Conference on Bioinformatics.

[41]  A. Rosowsky,et al.  Synthesis and Potent Antifolate Activity and Cytotoxicity of B-Ring Deaza Analogues of the Nonpolyglutamatable Dihydrofolate Reductase Inhibitor Nα-(4-Amino-4-deoxypteroyl)-Nδ-hemiphthaloyl-l-ornithine (PT523) , 1998 .

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

[43]  Thomas Lengauer,et al.  Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention , 1997, J. Comput. Aided Mol. Des..

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

[45]  Tad Hurst,et al.  Flexible 3D searching: The directed tweak technique , 1994, J. Chem. Inf. Comput. Sci..

[46]  J. Gasteiger,et al.  FROM ATOMS AND BONDS TO THREE-DIMENSIONAL ATOMIC COORDINATES : AUTOMATIC MODEL BUILDERS , 1993 .

[47]  Hans-Joachim Böhm,et al.  The computer program LUDI: A new method for the de novo design of enzyme inhibitors , 1992, J. Comput. Aided Mol. Des..