Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction.

[1]  John A. Nelder,et al.  A Simplex Method for Function Minimization , 1965, Comput. J..

[2]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[3]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[4]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[5]  J. Woessner,et al.  Matrix metalloproteinases and their inhibitors in connective tissue remodeling , 1991, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[6]  Kenneth M. Merz,et al.  Force Field Design for Metalloproteins , 1991 .

[7]  I. Kuntz Structure-Based Strategies for Drug Design and Discovery , 1992, Science.

[8]  R. Huber,et al.  The X‐ray crystal structure of the catalytic domain of human neutrophil collagenase inhibited by a substrate analogue reveals the essentials for catalysis and specificity. , 1994, The EMBO journal.

[9]  R. Wahl,et al.  1.56 Å structure of mature truncated human fibroblast collagenase , 1994, Proteins.

[10]  R. Huber,et al.  X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design. , 1995, European journal of biochemistry.

[11]  U. Ryde,et al.  Molecular dynamics simulations of alcohol dehydrogenase with a four‐ or five‐coordinate catalytic zinc ion , 1995, Proteins.

[12]  M Karplus,et al.  Zinc binding in proteins and solution: A simple but accurate nonbonded representation , 1995, Proteins.

[13]  M. Browner,et al.  Matrilysin-inhibitor complexes: common themes among metalloproteases. , 1996, Biochemistry.

[14]  M. Browner,et al.  Crystal structures of matrilysin-inhibitor complexes , 1995 .

[15]  P. Gottschall,et al.  Regulation of matrix metalloproteinase expressions in astrocytes, microglia and neurons. , 1996, Neuroimmunomodulation.

[16]  David S. Goodsell,et al.  Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 , 1996, J. Comput. Aided Mol. Des..

[17]  A. H. Drummond,et al.  Recent advances in matrix metalloproteinase inhibitor research , 1996 .

[18]  R. Sobel,et al.  Matrix Metalloproteinases in the Normal Human Central Nervous System, Microglial Nodules, and Multiple Sclerosis Lesions , 1996, Journal of neuropathology and experimental neurology.

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

[20]  William G. Stetler-Stevenson,et al.  Matrix Metalloproteinases , 1997, Drugs & aging.

[21]  R. Babine,et al.  MOLECULAR RECOGNITION OF PROTEIN-LIGAND COMPLEXES : APPLICATIONS TO DRUG DESIGN , 1997 .

[22]  M. Maccoss,et al.  Inhibition of stromelysin-1 (MMP-3) by P1'-biphenylylethyl carboxyalkyl dipeptides. , 1997, Journal of medicinal chemistry.

[23]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .

[24]  K Nadassy,et al.  Analysis of zinc binding sites in protein crystal structures , 1998, Protein science : a publication of the Protein Society.

[25]  R. Huber,et al.  Structure of malonic acid‐based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data , 1998, Protein science : a publication of the Protein Society.

[26]  K V Damodaran,et al.  Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase. , 1999, Journal of medicinal chemistry.

[27]  T. Blundell,et al.  X‐ray structure of human stromelysin catalytic domain complexed with nonpeptide inhibitors: Implications for inhibitor selectivity , 1999, Protein science : a publication of the Protein Society.

[28]  R. Poorman,et al.  Synthesis of a series of stromelysin-selective thiadiazole urea matrix metalloproteinase inhibitors. , 1999, Journal of medicinal chemistry.

[29]  H. V. Van Wart,et al.  Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors , 1999, Nature Structural Biology.

[30]  Robin Taylor,et al.  SuperStar: a knowledge-based approach for identifying interaction sites in proteins. , 1999, Journal of molecular biology.

[31]  A. Gearing,et al.  Design and therapeutic application of matrix metalloproteinase inhibitors. , 1999, Chemical reviews.

[32]  H Matter,et al.  Quantitative structure-activity relationship of human neutrophil collagenase (MMP-8) inhibitors using comparative molecular field analysis and X-ray structure analysis. , 1999, Journal of medicinal chemistry.

[33]  H. Tsuzuki,et al.  Homology modeling of gelatinase catalytic domains and docking simulations of novel sulfonamide inhibitors. , 1999, Journal of medicinal chemistry.

[34]  S H Kaufmann,et al.  Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads. , 2000, Journal of medicinal chemistry.

[35]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[36]  Robert Powers,et al.  Structure-based design of a novel, potent, and selective inhibitor for MMP-13 utilizing NMR spectroscopy and computer-aided molecular design , 2000 .

[37]  P. E. Van den Steen,et al.  Structural Characterization of the Catalytic Active Site in the Latent and Active Natural Gelatinase B from Human Neutrophils* , 2000, The Journal of Biological Chemistry.

[38]  B Cox,et al.  Application of high-throughput screening techniques to drug discovery. , 2000, Progress in medicinal chemistry.

[39]  J. Drews Drug discovery: a historical perspective. , 2000, Science.

[40]  W. Welsh,et al.  Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a novel class of piperazine-based stromelysin-1 (MMP-3) inhibitors: applying a "divide and conquer" strategy. , 2001, Journal of medicinal chemistry.

[41]  Yuan-Ping Pang,et al.  EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases , 2001, J. Comput. Chem..

[42]  K. Appelt,et al.  Matrix Metalloproteinase Inhibitors for Cancer Therapy , 2000, Cancer Drug Discovery and Development.

[43]  D. Moras,et al.  Crystal structure of the stromelysin-3 (MMP-11) catalytic domain complexed with a phosphinic inhibitor mimicking the transition-state. , 2001, Journal of molecular biology.

[44]  B. Fingleton,et al.  Matrix Metalloproteinase Inhibitors and Cancer—Trials and Tribulations , 2002, Science.

[45]  Oleksandr V. Buzko,et al.  Modified AutoDock for accurate docking of protein kinase inhibitors , 2002, J. Comput. Aided Mol. Des..