- 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.
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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
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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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