Case Studies for Phamaceutical and Biotechnology Research

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Target Modeling and Analysis

• Three-dimensional structure by homology modeling and functional characterization of Falcinpain-3: hemoglobinase from the malaria parasite, Plasmodium falciparum
• Tools and methods used in Discovery Studio® for the visualization, characterization and analysis of the electrostatic effects on the alkali-activated K+ channel, TASK-2
• Antibody Modeling: A quick reference guide to building Antibody homology models, and graphical identification and refinement of CDR loops in Discovery Studio
• Prediction of Binding Free energies: Application to Class 1 MHC- Peptide binding Free Energies Predictions based on
  homology models using Discovery Studio and Pipeline Pilot
• Protein-protein docking studies of alpha-lytic protease with 2 inhibitors using ZDOCKpro
• Automated de novo Electron density Map Tracing for the Structural Genomics Era
• High-throughput Structural Prediction and Functional Annotation of Proteomic Sequences
• Can we use homology models in protein-protein docking
• CASP6: ChiRotor and Looper for Side-Chain and Loop Optimization
• Creating a Smart Virtual Screen Protocol, Part I: Preparing the Target Protein
• Evolutionary Trace analysis of dihydrofolate reductase (DHFR)
• Flexible Docking of 3-Phenylpropylamine into Trypsin - an Affinity Validation Study
• Flexible Docking of Benzylsuccinate Inhibitor into Carboxypeptidase A - an Affinity Validation Study
• Flexible Docking of Biotin into Streptavidin - an Affinity Validation Study
• From Gene to Function: In Silico Warfare on the West Nile Virus
• High Throughput Functional Annotation of The Human Proteome
• Mass Spec Searching Against A Highly Annotated Protein Database
• Pipeline for functional annotation of novel proteins by structural homology
• Prediction and Analysis of Transmembrane Proteins Using Sequence Analysis Tools
• Structural and functional annotation of the Drosophila melanogaster genome: a case study for the "kinase" annotation
• Structural Prediction and Analysis of Alpha B-Crystallin, a Small Heat-shock Protein and Molecular Chaperone
• Structural prediction and functional annotation of proteomic sequences using DS GeneAtlas
• Understanding the SARS Genome/Proteome Using DS Gene, DS GeneAtlas, and DS AtlasStore

 

Lead Discovery and Optimization

• Automated De Novo Design Workflow with Physics-Based Scoring Function for Fast Lead Identification and Optimization
• Automated de novo Electron density Map Tracing for the Structural Genomics Era
• High-throughput Structural Prediction and Functional Annotation of Proteomic Sequences
• Creating a Smart Virtual Screening Protocol, Part II: Recursive Partitioning for Sequential Screening
• Creating a Smart Virtual Screening Protocol, Part III: Using Structure Based Drug Design to Enhance an In Silico Workflow
• Flexible Docking of 3-Phenylpropylamine into Trypsin - an Affinity Validation Study
• Flexible Docking of Benzylsuccinate Inhibitor into Carboxypeptidase A - an Affinity Validation Study
• Flexible Docking of Biotin into Streptavidin - an Affinity Validation Study
• Structural Analysis Of CDK2 Inhibitors Using Bayesian Modeling in Pipeline Pilot
• Discovery of novel insect repellent candidates with predictive pharmacophores identified with Accelrys’ Catalyst software environment
• Finding 'Bioactive' Conformations using Catalyst's Conformer Generation Algorithm
• Discovery of a Novel and Selective Cellular Inhibitor with Catalyst
• Discovery of a Potent, Novel, and Selective Inhibitor with Catalyst
• Identification of a Potent Non-Peptic Small Molecule Antagonist with Catalyst
• Using combined active and inactive data from HTS to reduce false positives and yield better enrichments (Catalyst)

• Computation of Ligand States in Preparation for Design Against Biological Targets
• Simple, Efficient Computational Tools to Facilitate Drug Discovery
• Automated Training Set Selection used for Developing a 3D QSAR Pharmacophore Model in CATALYST™ for p38 MAP Kinase inhibitors

 

Delivery and Formulation

• Crystal structure determination from conventional X-ray powder diffraction data of polycrystalline materials
• Crystal Structure Determination of N-(p-Tolyl)-dodecylsulfonamide at Kodak
• Crystal Structure Prediction of Diastereomeric Salts: A Step Towards the Rationalization of Racemate Resolution
• Crystal Structure Solution of a Metastable Polymorph from Powder X-Ray Diffraction Data
• Crystalline Component Identification From Simulated Powder X-Ray Diffraction Patterns
• Density Functional Theory Invetsigations of 17O Magnetic Resonance in Glutamic Acid Polymorphs
• Molecular Modeling Of The Crystal Cleavage Of Drugs And Pharmaceutical Excipients
• Crystal Structure Determination from Experimental Powder Data
• Formation of Isomorphic Desolvates
• X-Cell - a novel and robust indexing program for medium- to high-quality powder diffraction data
• Crystal Structure Determination from Conventional Powder Diffraction Data
• Potential Polymorphs of Aspirin
• Predicting the Polymorphs of Primidone and Progesterone
• Crystal Morphology Tools used in the Fight Against Malaria