|
Foster
City
 Applied
Biosystems announced the formation of a center for proteomics research
at its PerSeptive Biosystems Division. The Proteomics Research Center's
mission is to define novel tools for proteomics, focus on the advancement
of the science of proteomics, and develop practical application-based
systems for the fields of research, drug discovery and development,
and health care. |
Fremont
 Ciphergen
Biosystems, develops, manufactures, sells, and services ProteinChip¨
Systems and related products that discover, characterize and assay
proteins from native biological samples. Ciphergen customers include
many of the largest pharmaceutical and biotechnology companies worldwide,
as well as government agencies, research institutions, and universities.
Working with customers to develop new products and applications, Ciphergen
is becoming a leader in biomarker discovery, assay development and
characterization. |
 Proteome
BioKnowledge® Library Now part of the Incyte family of products,
the Proteome BioKnowledge Library is a powerful collection of databases
focused on the compilation of available protein information. Using
our proprietary processes, we comb through relevant biological literature
for curation into our products. The data are then presented in an
easy to use format that offers enhanced flexibility and powerful time
savings over traditional library research. Access to thousands of
independent research results offers the competitive advantage of reduced
library research time and faster progression through discovery pathways.
|
 LumiCyte,
Inc. is a biotechnology company focused on the discovery and routine
delivery of powerful new medical knowledge. LumiCyte uses its patented
Protein BioChips, BioChip Readers and informatics technologies to
enable the detection of disease earlier than ever before, more accurate
classification of disease type, better monitoring of disease progression
and more accurate and cost-effective monitoring of individual patient
response to therapy. LumiCyte collaborates with leading universities,
medical centers of excellence, and partners with companies to advance
the medical usefulness of its integrated protein separation, mapping
and analysis capabilities. LumiCyte's objectives are to enable and
accelerate successful drug development efforts and to help create
the diagnostic and therapeutic capabilities necessary to deliver individualized
medical care. |
Hayward
Lynx will apply its genomics, genetics, and proteomics technologies
to accelerate the pace, broaden the scale, enhance the quality, and
lessen the cost of the discovery and development efforts of customers
in the pharmaceutical and agricultural biotechnology industries. |
 Signature
BioScience is a development stage biotech company which is creating
a breakthrough technology platform for true functional proteomics.
Our system enables real-time, label-free observation of the activities
of proteins under their natural, unperturbed conditions. By embedding
our technology as a new component of the drug screening process, we
believe the pace and quality of discovery of both new drug targets
and new medicines will be significantly increased. Signature's drug
discovery strategy is to evaluate potential new targets and compounds
in parallel, and screen for specific physiologic activity at the earliest
points in the discovery process. This strategy has resulted in WaveScreen,
Signature's unique discovery platform that combines complementary
screening technologies with assays and chemistries to facilitate access
to a wide range of biological activities. Signature's proprietary
technologies include a microwave-based spectroscopy, known as MCS,
and Cytection, a high-throughput bioassay using primary human cells.
|
 Zyomyx
has developed technology that enables proteins to be analyzed with
the kind of precision and throughput that automated sequencers and
DNA chips brought to the study of our genes. Not just an adaptation
of DNA chip technology - the Zyomyx platform was designed from the
ground up for proteins. A result of over 250 man-years of focused
research and development, it is the only platform to deliver the needed
combination of biological specificity, high sample throughput, sensitivity,
and massive parallelism. The power of Zyomyx' technology will be utilized
by pharmaceutical and biotech companies to validate the backlog of
targets created by their genomics programs, to study the mechanism
of action for new drug leads, and to enable real time monitoring of
therapeutic response and potential side effects. It will also enable
diagnostics companies to move quickly, identify new biological markers,
and enable clinicians to run hundreds of tests from a single drop
of blood or small tissue samples. Given the flexibility and broad
applicability of the technology there will likely be numerous other
applications throughout life science research and in other fields.
Zyomyx will profit by supplying proteomics research tools and by collaborating
with others to apply them in pharmaceutical research. It will also
supply technology and components to other companies pursuing complementary
applications.
|
Hercules
 The
ProteomeWorks system is an integrated set of tools and technologies
that enables protein function discovery. Innovative new tools for
sample preparation, 2-D electrophoresis, staining, imaging and image
analysis, spot excision, automated protein digestion, mass spectrometry,
and bioinformatics create a seamlessly integrated, high-throughput
proteomics platform. |
La
Jolla
ActivX Biosciences is pioneering the field of activity-based proteomics
to increase the speed and cost-effectiveness of target discovery and
drug development. The company is developing a high-throughput chemistry
platform for identifying and analyzing active proteins in all ranges
of abundance in any biological sample. Current genomics and proteomics
technologies do not report on protein activity - an end-stage event
that regulates both health and disease. By providing the first global
analysis of protein activities, ActivX's next-generation proteomics
approach addresses the gap between the data generated by standard
genomics and proteomics techniques and the therapeutic relevance of
those data. |
Livermore
Protein
Structure Prediction Center (Lawrence Livermore National Lab) |
Los
Angeles
Protein Pathways is a privately held biotechnology company, founded
in 1999, that is a leader in the development of algorithms that can
be applied to the functional interpretation of sequenced genomes.
Our proprietary system of pathway elucidation is called the ProMaps™
discovery system. While most comparative genomics analyses are based
almost exclusively on similarity searches that infer only limited
aspects of biological function, the ProMaps™ discovery system
can predict gene function, place newly discovered genes in existing
pathways and elucidate interactions between pathways. In other words,
by using the ProMaps™ discovery system it is possible not only
to predict the biological classification of a gene product, but to
also gain insight into interacting proteins, the nature and identification
of probable substrates, and the biological context of the associated
pathway. The company has established the discovery of molecular interactions
as its core competency because of the firm belief that placing genes
in existing pathways and understanding the network interactions between
pathways will inevitably lead to improved methods that facilitate
the small molecule drug discovery process. |
| UCLA-DOE
Lab of Structural Biology (U California-Los Angeles) |
|
Mountain
View
ACLARA
BioSciences
ACLARA is a pioneer in the field of microfluidics, or lab-on-a-chip
technology, with access to the wide range of technology and intellectual
property required to broadly address key markets such as genomics
(RNA and DNA analysis), proteomics, multiplexed DNA sample preparation
and pharmaceutical drug screening. To penetrate these large and
rapidly growing markets, we are developing multiple products that
incorporate microfluidics, the controlled movement of small volumes
of fluids through an array of microscopic channels on ACLARA's disposable
plastic LabCard™ chip products. Additionally, ACLARA is developing
unique and proprietary chemistries that will enable key applications.
These technologies are designed to allow researchers to rapidly
perform large numbers of chemical and biological measurements in
a miniaturized, integrated and automated format.
|
 Caliper
is a leader in lab-on-a-chip technologies. We develop, manufacture
and sell our proprietary microfluidic LabChip® systems to pharmaceutical
and other companies. We believe our LabChip systems can assemble the
power of entire laboratories full of equipment and people. Our LabChip
systems miniaturize, integrate and automate many laboratory processes,
and put them on a chip that can fit in the palm of a child's hand.
Each chip contains a network of microscopic channels through which
fluids and chemicals are moved in order to perform experiments. We
believe our LabChip systems represent a revolutionary advance in laboratory
experimentation. |
 Cognia
is a developer and distributor of knowledge-based products that facilitate
the use of genomic, proteomic and cellomic/physiological information.
Cognia provides integrated suites of high-quality, annotated databases,
cutting edge bioinformatic tools, and associated consulting services
to accelerate drug discovery and basic research. |
 SurroMed's
platform for biological marker discovery incorporates proprietary
technologies for profiling and analyzing thousands of immune cell
populations, proteins and low-molecular-weight organic molecules in
small volumes of blood and/or other biological samples. By capturing,
integrating and analyzing large amounts of clinical and biological
informationÑat the level of the cell, gene, protein, and low-molecular-weight
organic moleculeÑSurroMed is able to identify useful biological markers
and provide a detailed picture, or "fingerprint," of pathways involved
in disease and therapeutic response. SurroMed analyzes samples in
its Biomarker Discovery Laboratory under stringent quality control
procedures designed to ensure sample accountability and data integrity.
|
Palo
Alto
Proteome
BioKnowledge® Library Now part of the Incyte family of products,
the Proteome BioKnowledge Library is a powerful collection of databases
focused on the compilation of available protein information. Using
our proprietary processes, we comb through relevant biological literature
for curation into our products. The data are then presented in an
easy to use format that offers enhanced flexibility and powerful time
savings over traditional library research. Access to thousands of
independent research results offers the competitive advantage of reduced
library research time and faster progression through discovery pathways.
|
 Life
Sciences/Chemical Agilent is a leading provider of life sciences and
analytical instrument systems to scientists in life sciences, pharmaceutical,
environmental and chemical industries, worldwide. The company offers
scientists the range of instruments, systems and services needed for
success in acquiring and interpreting genetic and chemical information
- from sample handling, to analysis to data management and reporting.
We are committed to providing superior standards-based technology,
designed for maximum productivity, cost effectiviness and ease in
complying with regulatory requirements. |
Redwood
City
 Scimagix
ProteinMin™ is designed to extract, analyze and mine protein
image-data from 2D electrophoresis gels. It extracts an index of the
visual characteristics of a 2D gel experiment and places it into a
database. The proteomics scientists can then query their entire collection
of gel experiments to find similar "protein signatures." The first
of a series of plug-in modules for SIMS, ProteinMine features: Automatic
spot detection; Unwarping; Easy user interface for manual adjustments;
Automatic registration of all spots into Oracle; Ability to search
all experiments for "protein signatures" |
San
Diego
 Our
comprehensive computational chemistry and structural biology services
help you get the most from your synthesis and screening programs.
We believe that optimal lead discovery and optimization is the result
of a continual thorough analysis and understanding of all relevant
structural, chemical, and biological information. Our proprietary
methods enable this critical understanding of the target, its ligands,
and the target-ligand relationship. When the structure of the target
is known we employ proprietary structure based design methods. Our
Token™, technology is used to characterize and compare protein
surfaces. Through this analysis we can design for affinity and specificity
reducing the likelihood of undesirable crossreactivity and late stage
clinical failure. Using SurFlex™ Dock and Refinery™ we are
also able to rapidly perform and analyze virtual screening experiments
to identify meaningful leads for biological screening. When the structure
of the target is not known, we employ proprietary ligand based design
methods to design and rapidly analyze the results of high throughput
screening experiments. Initial screening compounds may be selected
to be similar to known ligands, or maximally diverse when little or
no ligand information is available. Screening results are rapidly
analyzed using Support Vector Machine algorithms which are able to
determine which features of a molecule correlate best with activity,
and those which correlate with inactivity. This knowledge is then
used to formulate a Structure Activity Relationship which guides compound
synthesis for follow on screening. |
 BIOSITE'S
IMMEDIATE RESPONSE DIAGNOSTICS™ TECHNOLOGY is based on proprietary
advances in several core scientific and engineering disciplines, including
antibody development and engineering, analyte cloning and synthesis,
signaling chemistry and micro capillary fluidics. The Company has
utilized its core technologies to develop two distinct product platforms:
The Triage Panel for qualitative visual readings and the Triage Meter
System for quantitative measurements. The Company's products are designed
to measure either a single analyte or multiple analytes simultaneously
and to allow for the qualitative or quantitative analysis of various
samples, including urine, serum, plasma, whole blood and stool. Both
of the product platforms are designed to provide rapid results, ease
of use, high analytical accuracy and the capability of performing
multiple analyses in a reliable testing device. |
 GeneFormatics
Incorporated, a world leader in structural proteomics, focuses on
providing novel protein function and structure information to pharmaceutical,
biotechnology and agrochemical companies to accelerate the discovery
of new medicines and other useful products. GeneFormatics applies
its integrated, "function first," high throughput proteomics platform,
which combines in silico technologies, NMR spectroscopy, X-ray crystallography
and bioassays, on genomic scales to assign protein function and determine
protein structure. |
 Structural
Bioinformatics, Inc. (SBI) is a world leader in proteomics-driven
drug discovery the large-scale generation and use of protein structural
information to accelerate the discovery and optimization processes.
SBIÕs Genes to Leads¨ technology, employing SBIÕs proprietary DynaPharm®
and CombiLib® technologies, offers a truly practical response
to the wealth of new drug targets emerging from genomic sequencing
efforts around the world for the human genome and the genomes of hundreds
of infectious disease agents. Our technology reliably produces drug
leads in 60-120 days starting with the sequence alone, with an efficiency
that is more than 1,000-fold greater than state-of-the-art high throughput
screening (HTS). The efficiencies in speed and cost are the direct
result of the use of our underlying proprietary computational proteomics
platform that allows us to generate X-ray quality protein structures
at a fraction of the cost and time. We further leverage our proteomics,
pattern recognition, and data fusion technologies through our structural
database products: the ProMax™ drug target database - containing
thousands of proprietary drug target and Òanti-targetÓ structures
in more than 470 structural families; the Variomeª family of structural
polymorphism databases containing tens of thousands of unique polymorphism
structures - providing pharmacogenomics insights early on in the drug
discovery process; and StructureBank™ a universal repository
and enterprise-wide solution for large-scale storage and comparative
analysis of protein structures. |
 Structural
GenomiX (SGX) is revolutionizing the use of protein structure in the
drug discovery process, helping to create safer, more effective medicines.
Using high-throughput structural biology, SGX is translating the wealth
of genetic and genomic information generated over recent years into
structural templates for drug discovery, on an industrial scale. Availability
of the 3-dimensional structure of a protein target can aid drug discovery
at many points in the process, particularly in lead discovery and
optimization, as well as at the earlier stages of target identification
and validation. |
 Syrrx,
Inc. is a drug discovery company committed to redefining the way medicines
is discovered. Based in San Diego, CA, the company is at the forefront
of high-throughput rational drug discovery. Syrrx intends to leverage
high-throughput structure determination, high-throughput screening,
combinatorial and medicinal chemistry together with computational
methods to discover novel small molecule preclinical drug candidates.
This process enables a unique "gene to drug" platform based on the
ability to perform high-throughput rational drug discovery. |
 Accelrys
(formerly Molecular Simulations Inc.) delivers software and services
based on its industry-leading expertise in informatics and computation
for the biological, chemical, and materials sciences. The result is
the accelerated design, discovery, and development of pharmaceuticals,
chemicals, and materials. Accelrys meets these needs with an unrivalled
portfolio of technology, expertise developed through years of success
in developing and applying scientific software, a worldwide scientific
and sales presence, financial strength, and active partnerships with
major pharmaceutical, biotechnology, and chemical companies. Accelrys
is a subsidiary of Pharmacopeia Inc. |
San
Francisco
 GeneData
is a global leader in the development of bioinformatics systems and
related services in the functional genomics arena. We deliver innovative
computational solutions for the management and intelligent analysis
of large quantities of structurally complex biological data, generated
by genome sequencing, microarrays, protein expression profiling, metabolic
profiling and high-throughput screening. Our partners include major
life-sciences organizations and some of the world's most prestigious
research institutions. We strive to help our partners maximize their
return on investment from costly technologies and gain a deeper understanding
of underlying biological processes for advancement of their own research
and product development. Founded in 1997, GeneData has grown to a
team of around 70 experts from diverse fields including molecular
biology, biochemistry, computer science, (bio)physics, mathematics
and statistics. Our growth continues as we recruit the best people
for developing and applying in-silico methods for functional genomics
problems. |
| Cohen
Lab (U California San Francisco) |
San
Jose
Applied
Biosystems announced the formation of a center for proteomics research
at its PerSeptive Biosystems Division. The Proteomics Research Center's
mission is to define novel tools for proteomics, focus on the advancement
of the science of proteomics, and develop practical application-based
systems for the fields of research, drug discovery and development,
and health care. |
 Thermo
Finnigan, a Thermo Electron business, supports laboratory professionals
with the most reliable products and services available. Thermo Finnigan
makes mass spectrometry and chromatography equipment, among the most
accurate and sensitive available, for analyzing a wide array of substances.
The business is one of the world's leading manufacturers of these
instruments, which separate, identify, and quantify natural products,
chemical mixtures and biological samples. The business serves markets
totaling an estimated $8 billion worldwide. |
Santa
Cruz
Computational
Biology Group (U California Santa Cruz) |
Stanford
Brutlag Bioinformatics
Group (Stanford) |
| Levitt
Lab (Stanford) |
| Pande
Group, Stanford University (Folding@Home) |
Sunnyvale
 Compugen
develops and markets platforms, tools and products that accelerate
post genomic research, the advanced study of proteins and protein
pathways, and drug target discovery.
|
Vacaville
 Large
Scale Biology Corporation (LSBC) is one of world's leading companies
dedicated to the discovery, analysis, manufacture and commercialization
of proteins Ñ the molecules at the business end of biology. LSBC's
activities are built around an integrated suite of ultra-sensitive,
industrial-scale technologies created to realize the full commercial
and pharmaceutical potential of biology. LSBC's proprietary technologies
radically extend the power of genomics. Whereas traditional genomics
companies concentrate on deciphering genetic information, LSBC goes
further, directly analyzing, manipulating and manufacturing the proteins
that the genetic information encodes. Proteins are at the heart of
all biological processes, and LSBC's unique protein-focused technologies
have placed the company at the forefront of the drive to bring twenty-first
century biology to the marketplace. |
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