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Contents on the CD Rom

  • Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. Its aim is the prediction of the three-dimensional structure of proteins from their amino acid sequences, sometimes including additional relevant information such as the structures of related proteins.
  • The complexes of two or more proteins, where the structures of the proteins are known or can be predicted with high accuracy, protein-protein docking methods can be used to predict the structure of the complex.
  • Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures. In each case, a scoring function is used to assess the compatibility of the sequence to the structure, thus yielding possible three-dimensional models. This type of method is also known as 3D-1D fold recognition.
  • Crystallography plays a major role in current efforts towards protein structure determination. Building a protein model from crystallographic data, however, is a complex and time-consuming process, which is somewhat assisted by the use of computer graphics for tracing the polypeptide chains, and for viewing and improving the resulting model.
  • The great majority of drugs that are available today perturb the activity of physiological processes by interrupting or facilitating a biochemical pathway.
  • The wire-bender of Rubin and Richardson is a convenient tool for constructing carbon models of proteins. It has been used in laboratories for building protein backbone models which helped us establish the existence of continuous regions of peptide chain in globular proteins.
  • X-ray crystallography is the main method for structure determination of proteins. This can be a time-consuming process, and it will succeed only if it is possible to find suitable conditions for growing crystals.
  • Homology modelling has significant potential as a tool in rational drug design, in particular in high throughput in silico screening or simulation approaches.
  • In drug design, one faces the problem to predict reasonably which molecules from a pool of millions of possible compounds will interact with a target of medical or biological interest. One approach is to utilize 3D-models of target proteins and ligands. In order to build reasonable and useful models, as much information as possible has to be incorporated into the modelling process.
  • Homology or comparative protein structure modeling constructs a three-dimensional model of a given protein sequence based on its similarity to one or more known structures.
  • Protein structure prediction is of high importance in medicine and biotechnology.
  • Homology-based rational drug design is a useful tool for the pharmaceutical industry.
  • The application of the techniques of molecular biology, transgenics, knockouts and antisense have led to many advances in our understanding of drug action, and indeed to the development of new drugs.
  • Knowledge of the three-dimensional (3D) structure of protein-protein complexes provides a valuable systems. The rate of protein structure
    determination is increasing rapidly.
  • The development of a new drug, or medicine, is a challenge of tremendous complexity and of truly multi-disciplinary character. It is currently also of a dual nature. Typical trialand error processes are carried out simultaneously with the most advanced biochemical synthetic and computational procedures.
  • A rational drug design is good to remember the long list of obstacles to be overcome before a compound showing a desired activity in a test tube can be sold on the market as a useful drug. Drug delivery and safety, possibilities of metabolic alterations and economics of production all need to be given great attention and are time-consuming. The great advantage of this strategy shows a considerable percentage of new drugs coming on the market.
General
  • Protein structure prediction
  • High-Resolution Protein Structure Prediction
  • The Proteome, Bioinformatics and Drug Discovery
  • Homology Modeling
  • Integrating Bioinformatics, Medical Sciences and Drug Discovery
  • Improving Sequence Alignment For Protein Modelling

Structure and Process

  • Comparative protein structure modeling
  • Protein Model Determination from Crystallographic Data
  • Modelling Protein Docking using Shape Complementarity, Electrostatics and Biochemical Information
  • The molecular mechanisms of drug action
  • Minimization of Construction Errors in Bent-Wire Protein Models
  • Homology-Based Modelling of Targets for Rational Drug Design
  • A structural keystone for drug design
  • Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria
  • Modelling fat and protein concentration curves for Irish dairy cows
  • Modelling Protein-Protein Interaction Networks via a Stickiness Index
  • Homology modelling & visualization of protein structure
  • The Challenge of Protein Modelling
  • Structural Classification of Proteins
  • Comparative protein modelling-Introduction
  • De novo modelling of G-protein coupled receptors
  • Tertiary Protein Structure and folds
  • Quaternary Structure
  • Secondary structure and backbone conformation
  • Super-secondary structure

Company Profiles

  • Company in Gent
  • Company in France
  • Company in Netherlands
  • Company in California
  • Another Company in California

Lab

  • Lab in Portugal
  • Lab in California
  • Lab in San Francisco
  • Lab in UK
  • Lab in Israel
  • Lab in New Jersey
  • Biomolecular Modelling Lab

Consultants

  • Consultant in California
  • Expert in Protein- and Peptide-Based Drug Discovery, Protein Assay Development, Cell Biology, and Immuno-Blot
  • Consultant in Indiana
  • Forensic Bioinformatics Staff
  • Project Consultant
  • Service Providers in the Field of Biotechnology

Patent

  • Application of protein structure predictions
  • Method and System for Protein Modeling
  • Protein Modification to provide enzyme activity
  • Protein Molecule Model

Technology

  • Development of Protein Profile Technology to Evaluate Ecological Effects of Environmental Chemicals Using a Small Fish Model
  • Biomolecular modelling from drug discovery to nanotechnology
  • Xencor Expands Protein Optimization Technology To Develop Next-Generation Biotechnology Products
  • The role of in silico approaches in modern drug discovery
  • Molecular Modeling Databases: A New Way in the Search of Protein Targets for Drug Development
  • Technology/Business Opportunity Protein Structure Modeling
  • MeCAT - Absolute Protein Quantification Technology
  • Tactile Teaching: Exploring Protein Structure/Function Using Physical Models
Functions
  • Evolutionary model for predicting protein function by matching local surfaces: a Bayesian Monte Carlo
    approach
  • Modeling Protein Function
  • A Graphical Model for Predicting Protein Molecular Function
  • Stability and the Evolvability of Function in a Model Protein
  • A Thermodynamic Model for Prebiotic Protein Function

Thesis

  • Comparative Analysis of Protein Classification Methods
  • Protein cross-linking with oxidative enzymes and transglutaminase
  • Dissolved Protein Modification and Degradation in Natural Waters
  • Hidden Markov Models for Remote Protein Homology Detection
  • Analysis and modelling of protein interaction networks
  • Roadmap Analysis of Protein-Protein Interactions

Project

  • Computational Modeling of pH dependent Protein Structures
  • Construction of a Protein Family Data Base
  • Protein Function Prediction by Matching Volumetric Models of Active Sites
  • Modeling Protien-Protein Interactions with the Aid of Motion Planning Algorithms
  • Market Impacts of High-Protein Whey Product Promotion

Applications

  • Application of the Cornell Net Carbohydrate and Protein model for cattle consuming forages
  • Cheminformatic in Pharmaceutical Industry
  • Accuracy and application of protein structure models
  • Comparative Protein Structure Modeling and its Applications to Drug Discovery

Tools and Server

  • Autopsy of a PDB file
  • Bioinformatic Tools
  • D-JIGSAW Protein Comparative Modelling Server
  • MatchMakerTM
  • ModLoop: automated modeling of loops in protein structures
  • Structure prediction servers
  • RAPPER: Protein Modelling Server
  • SWISS-MODEL: an automated protein homology-modeling server
  • Swiss-PdbViewer
  • Web based application for Protein Modeling
  • RECCR WebPDB pdb pre-processing web tool
  • How to do Standalone Modelling
  • Limitations of the Modelling

Report

  • Drug Discovery for Molecular Science
  • Protein crystallography, computer graphics and drug design
  • New Paradigms in Computational Chemistry for Drug Discovery
  • Chance favors the prepared mind - From Serendipity to rational drug design
  • Sixth Australian/Japan Symposium on Drug Design and Development
  • The GRIDs @ Novartis
  • The Mapping of the Human genome: Where next? An analysis and Point of view
  • Molecular modelling probes: docking and scoring
  • Advanced Protein Modeling
  • Protein modeling and structure prediction with a reduced representation

Guidelines

  • Modeling Laboratory Dictionary of Terms for Molly
  • Protein Folding - Introductions and Surveys

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