Homology modeling in drug discovery: current trends and applications.
暂无分享,去创建一个
Claudio N. Cavasotto | Sharangdhar S. Phatak | Claudio N Cavasotto | Sharangdhar S Phatak | C. Cavasotto
[1] N. Cohen,et al. Structure-based drug design and the discovery of aliskiren (Tekturna): perseverance and creativity to overcome a R&D pipeline challenge. , 2007, Chemical biology & drug design.
[2] David C Fry,et al. Protein-protein interactions as targets for small molecule drug discovery. , 2006, Biopolymers.
[3] M. Mueckler,et al. Transmembrane Segment 6 of the Glut1 Glucose Transporter Is an Outer Helix and Contains Amino Acid Side Chains Essential for Transport Activity* , 2008, Journal of Biological Chemistry.
[4] V. Kairys,et al. Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement , 2006, TheScientificWorldJournal.
[5] Alessandra Gianoncelli,et al. Identification of novel protein kinase CK1 delta (CK1delta) inhibitors through structure-based virtual screening. , 2008, Bioorganic & medicinal chemistry letters.
[6] Jörg Rademann,et al. Specific inhibitors of the protein tyrosine phosphatase Shp2 identified by high-throughput docking , 2008, Proceedings of the National Academy of Sciences.
[7] Mihaly Mezei,et al. Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2. , 2008, Journal of medicinal chemistry.
[8] Rick Gussio,et al. Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore. , 2006, Bioorganic & medicinal chemistry.
[9] Thomas A. Halgren,et al. Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..
[10] S. Moro,et al. Ligand-based homology modeling as attractive tool to inspect GPCR structural plasticity. , 2006, Current pharmaceutical design.
[11] Krzysztof Palczewski,et al. Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm , 2022 .
[12] Bruno O Villoutreix,et al. Proposed structural models of the prothrombinase (FXa–FVa) complex , 2006, Proteins.
[13] J. Skolnick,et al. How well is enzyme function conserved as a function of pairwise sequence identity? , 2003, Journal of molecular biology.
[14] H Kubinyi. HTS Technologies--IBC Informa Conference. , 2001, IDrugs : the investigational drugs journal.
[15] A. Anderson. The process of structure-based drug design. , 2003, Chemistry & biology.
[16] J. Nosanchuk,et al. Biological Function and Molecular Mapping of M Antigen in Yeast Phase of Histoplasma capsulatum , 2008, PloS one.
[17] Claudio N. Cavasotto and Narender Singh. Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility , 2008 .
[18] Nir Ben-Tal,et al. Model Structure of the Na+/H+ Exchanger 1 (NHE1) , 2007, Journal of Biological Chemistry.
[19] Mohammed A Kashem,et al. Discovery of potent and selective PKC-theta inhibitors. , 2007, Bioorganic & medicinal chemistry letters.
[20] John O Trent,et al. Small-molecule inhibition of 6-phosphofructo-2-kinase activity suppresses glycolytic flux and tumor growth , 2008, Molecular Cancer Therapeutics.
[21] Matthieu Schapira,et al. Structural genomics and drug discovery: all in the family. , 2008, Current opinion in chemical biology.
[22] Hwangseo Park,et al. Discovery of novel Cdc25 phosphatase inhibitors with micromolar activity based on the structure-based virtual screening. , 2008, Journal of medicinal chemistry.
[23] Daniel Fischer,et al. Servers for protein structure prediction. , 2006, Current opinion in structural biology.
[24] Claudio N. Cavasotto,et al. Scalaradial, a Dialdehyde‐Containing Marine Metabolite That Causes an Unexpected Noncovalent PLA2 Inactivation , 2007, Chembiochem : a European journal of chemical biology.
[25] Ana M. Rojas,et al. The Nod-Like Receptor (NLR) Family: A Tale of Similarities and Differences , 2008, PloS one.
[26] Hermann Schindelin,et al. Structural and Mechanistic Insights into Lunatic Fringe from a Kinetic Analysis of Enzyme Mutants* , 2009, Journal of Biological Chemistry.
[27] Jacquelyn S Fetrow,et al. Structure-based active site profiles for genome analysis and functional family subclassification. , 2003, Journal of molecular biology.
[28] Marc A. Martí-Renom,et al. MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..
[29] Konrad Büssow,et al. Automated technologies and novel techniques to accelerate protein crystallography for structural genomics , 2008, Proteomics.
[30] Claudio N. Cavasotto,et al. Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking , 2005 .
[31] C. Cavasotto,et al. The binding mode of petrosaspongiolide M to the human group IIA phospholipase A(2): exploring the role of covalent and noncovalent interactions in the inhibition process. , 2009, Chemistry.
[32] Steven M. Muskal,et al. Interrogating the Druggable Genome with Structural Informatics , 2007 .
[33] K. Lundstrom,et al. Structural genomics and drug discovery , 2007, Journal of cellular and molecular medicine.
[34] Hiroki Shirai,et al. Identification of the Druggable Concavity in Homology Models Using the PLB Index , 2007, J. Chem. Inf. Model..
[35] Emil Alexov,et al. Predicting 3D structures of transient protein-protein complexes by homology. , 2006, Biochimica et biophysica acta.
[36] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[37] M. Jacobson,et al. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. , 2005, Biochemistry.
[38] Michael Levitt,et al. Growth of novel protein structural data , 2007, Proceedings of the National Academy of Sciences.
[39] Lupei Du,et al. Computational studies of the binding site of α1A-adrenoceptor antagonists , 2008, Journal of molecular modeling.
[40] Emil Alexov,et al. omology-based modeling of 3 D structures of protein – protein complexes using lignments of modified sequence profiles etras , 2008 .
[41] Tom L. Blundell,et al. Keynote review: Structural biology and drug discovery , 2005 .
[42] E. Hazai,et al. Homology modeling of breast cancer resistance protein (ABCG2). , 2008, Journal of structural biology.
[43] Udo Höweler,et al. Simulations of a G protein‐coupled receptor homology model predict dynamic features and a ligand binding site , 2008, FEBS letters.
[44] P. Fernandes,et al. Technological advances in high-throughput screening. , 1998, Current opinion in chemical biology.
[45] Richard M. Jackson,et al. An evaluation of automated homology modelling methods at low target-template sequence similarity , 2007, Bioinform..
[46] R. Hilgenfeld,et al. Utility of homology models in the drug discovery process , 2004, Drug Discovery Today.
[47] Dora M Schnur. Recent trends in library design: 'rational design' revisited. , 2008, Current opinion in drug discovery & development.
[48] Catherine L. Worth,et al. Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[49] Claudio N. Cavasotto,et al. Ligand docking and structure-based virtual screening in drug discovery. , 2007, Current topics in medicinal chemistry.
[50] Claudio N. Cavasotto,et al. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. , 2008, Journal of medicinal chemistry.
[51] Hugo O Villar,et al. Using NMR for ligand discovery and optimization. , 2004, Current opinion in chemical biology.
[52] Sebastian Radestock,et al. Homology Model-Based Virtual Screening for GPCR Ligands Using Docking and Target-Biased Scoring , 2008, J. Chem. Inf. Model..
[53] Hwangseo Park,et al. Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure. , 2008, Bioorganic & medicinal chemistry.
[54] Stefano Costanzi,et al. On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor. , 2008, Journal of medicinal chemistry.
[55] K. Ginalski. Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.
[56] Mario G. Cardozo,et al. Discovery of potent and selective PKC-θ inhibitors , 2007 .
[57] G. Montelione,et al. Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers. , 2008, Structure.
[58] Marcel L Verdonk,et al. Automated Protein–Ligand Crystallography for Structure‐Based Drug Design , 2006, ChemMedChem.
[59] Ning Ren,et al. Molecular modeling aided design of nicotinic acid receptor GPR109A agonists. , 2008, Bioorganic & medicinal chemistry letters.
[60] David P. Westfall. Adrenoceptor Antagonists , 2003 .
[61] Claudio N. Cavasotto,et al. Protein flexibility in ligand docking and virtual screening to protein kinases. , 2004, Journal of molecular biology.
[62] T. Blundell,et al. Structural biology and drug discovery. , 2005, Drug discovery today.
[63] Jianlin Cheng. A multi-template combination algorithm for protein comparative modeling , 2008, BMC Structural Biology.
[64] Hong Zhu,et al. Discovery of [7-(2,6-dichlorophenyl)-5-methylbenzo [1,2,4]triazin-3-yl]-[4-(2-pyrrolidin-1-ylethoxy)phenyl]amine--a potent, orally active Src kinase inhibitor with anti-tumor activity in preclinical assays. , 2007, Bioorganic & medicinal chemistry letters.
[65] Stefano Moro,et al. Linear and Nonlinear 3D-QSAR Approaches in Tandem with Ligand-Based Homology Modeling as a Computational Strategy To Depict the Pyrazolo-Triazolo-Pyrimidine Antagonists Binding Site of the Human Adenosine A2A Receptor , 2008, J. Chem. Inf. Model..
[66] John D. Westbrook,et al. The Protein Model Portal , 2008, Journal of Structural and Functional Genomics.
[67] Gerhard Klebe,et al. Development of Benzophenone‐Based Farnesyltransferase Inhibitors as Novel Antimalarials , 2008, ChemMedChem.
[68] Ashish V. Tendulkar,et al. Functional sites in protein families uncovered via an objective and automated graph theoretic approach. , 2003, Journal of molecular biology.
[69] Claudio N. Cavasotto,et al. 2,3‐Dihydro‐1‐Benzofuran Derivatives as a Series of Potent Selective Cannabinoid Receptor 2 Agonists: Design, Synthesis, and Binding Mode Prediction through Ligand‐Steered Modeling , 2009, ChemMedChem.
[70] Arne Elofsson,et al. Using multiple templates to improve quality of homology models in automated homology modeling , 2008, Protein science : a publication of the Protein Society.
[71] Robert C. Edgar,et al. Multiple sequence alignment. , 2006, Current opinion in structural biology.
[72] Francesco Musiani,et al. A model‐based proposal for the role of UreF as a GTPase‐activating protein in the urease active site biosynthesis , 2007, Proteins.
[73] Heidi J. Imker,et al. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. , 2007, Nature chemical biology.
[74] Ram Samudrala,et al. Improving the accuracy of template-based predictions by mixing and matching between initial models , 2008, BMC Structural Biology.
[75] Sharangdhar S. Phatak,et al. 6-Methoxy-N-alkyl isatin acylhydrazone derivatives as a novel series of potent selective cannabinoid receptor 2 inverse agonists: design, synthesis, and binding mode prediction. , 2009, Journal of medicinal chemistry.
[76] Claudio N. Cavasotto,et al. Structure-based development of target-specific compound libraries. , 2006, Drug discovery today.
[77] D. Langley,et al. Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach , 2008, Proteins.