IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface

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

[2]  Álvaro Cortés Cabrera,et al.  VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface , 2011, J. Comput. Aided Mol. Des..

[3]  George Karypis,et al.  Common Pharmacophore Identification Using Frequent Clique Detection Algorithm , 2009, J. Chem. Inf. Model..

[4]  S. Stanley Young,et al.  Automated Pharmacophore Identification for Large Chemical Data Sets. , 1999 .

[5]  Jürgen Bajorath,et al.  New methodologies for ligand-based virtual screening. , 2005, Current pharmaceutical design.

[6]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[7]  Jun Feng,et al.  PharmID: Pharmacophore Identification Using Gibbs Sampling , 2006, J. Chem. Inf. Model..

[8]  K. Shadan,et al.  Available online: , 2012 .

[9]  Rafael Ordog PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins , 2008, Bioinformation.

[10]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[11]  M F Sanner,et al.  Python: a programming language for software integration and development. , 1999, Journal of molecular graphics & modelling.

[12]  W. Delano The PyMOL Molecular Graphics System , 2002 .

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

[14]  Gisbert Schneider,et al.  NIPALSTREE: A New Hierarchical Clustering Approach for Large Compound Libraries and Its Application to Virtual Screening , 2006, J. Chem. Inf. Model..

[15]  Cheng Luo,et al.  Discovery and SAR of thiazolidine-2,4-dione analogues as insulin-like growth factor-1 receptor (IGF-1R) inhibitors via hierarchical virtual screening. , 2010, Journal of Medicinal Chemistry.

[16]  Ruth Nussinov,et al.  PharmaGist: a webserver for ligand-based pharmacophore detection , 2008, Nucleic Acids Res..

[17]  Dimitris K. Agrafiotis,et al.  Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification , 2007, J. Chem. Inf. Model..

[18]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[19]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Thomas Lengauer,et al.  Novel technologies for virtual screening. , 2004, Drug discovery today.

[21]  J. Gums,et al.  Dabigatran Etexilate: A Novel Oral Thrombin Inhibitor for Thromboembolic Disease , 2011, The Annals of pharmacotherapy.

[22]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[23]  Brian K. Shoichet,et al.  Virtual screening of chemical libraries , 2004, Nature.

[24]  J. Irwin,et al.  Benchmarking sets for molecular docking. , 2006, Journal of medicinal chemistry.

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

[26]  Scott A. Busby,et al.  A Combined Ligand‐ and Structure‐Based Virtual Screening Protocol Identifies Submicromolar PPARγ Partial Agonists , 2011, ChemMedChem.

[27]  Bert L. de Groot,et al.  Ligand docking and binding site analysis with PyMOL and Autodock/Vina , 2010, J. Comput. Aided Mol. Des..

[28]  Santosh A. Khedkar,et al.  Pharmacophore modeling in drug discovery and development: an overview. , 2007, Medicinal chemistry (Shariqah (United Arab Emirates)).

[29]  Xin Chen,et al.  Automated Pharmacophore Identification for Large Chemical Data Sets1 , 1999, J. Chem. Inf. Comput. Sci..

[30]  Olivier Lichtarge,et al.  PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes , 2010, Bioinform..

[31]  CHUN WEI YAP,et al.  PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints , 2011, J. Comput. Chem..

[32]  Xin Chen,et al.  Discovery of Novel Pim-1 Kinase Inhibitors by a Hierarchical Multistage Virtual Screening Approach Based on SVM Model, Pharmacophore, and Molecular Docking , 2011, J. Chem. Inf. Model..

[33]  Maria João Ramos,et al.  Virtual screening in drug design and development. , 2010, Combinatorial chemistry & high throughput screening.

[34]  Ruth Nussinov,et al.  Deterministic Pharmacophore Detection Via Multiple Flexible Alignment of Drug-Like Molecules , 2007, RECOMB.

[35]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[36]  T. Tuccinardi Docking-based virtual screening: recent developments. , 2009, Combinatorial chemistry & high throughput screening.

[37]  Peter Willett,et al.  GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D , 2006, J. Comput. Aided Mol. Des..

[38]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.