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Case Studies for Pharmaceutical 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 cass 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 screening 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
- Determination of relative interaction energies of carbocyclic analogues
- 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
- 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)
- Automated training set selection used for developing a 3D QSAR pharmacophore model in Catalyst for p38 MAP kinase inhibitors
Delivery and Formulation
- Simulation of non-ionic surfactant micelles for controlled drug release
- 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 investigations 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
