Molecular Simulations Incorporated Company Profile

08:01 EST 24th November 2017 | BioPortfolio

Molecular Simulations Inc., a subsidiary of Pharmacopeia, Inc., is a leading provider of molecular modeling, simulation, and informatics software to the world’s foremost pharmaceutical, biotechnology, and chemical R&D facilities. Using MSI’s software and services, researchers can organize and analyze scientific data, share biological and chemical information, and develop novel compounds, materials, and processes. MSI employs over 325 people, nearly half of whom are Ph.D. scientists. Company headquarters are in San Diego, California. Major regional operations are in Cambridge, England, and Tokyo, Japan.

MSI’s Technology

Industrial R&D organizations strive to accelerate product discovery and development, reduce costs, improve processes, and address environmental standards. Computer simulation helps to achieve these goals — guiding scientists to new solutions and focusing experiments on the most productive pathways. Molecular simulation is the most fundamental simulation strategy; it allows researchers to predict the structures and properties of chemicals, biological compounds, and materials. MSI’s software combines this technology with high quality graphics visualization and informatics tools that maximize the utility of chemical and genomic databases.

Founded in Science

MSI has established a reputation as the leader in the scientific development and commercial implementation of simulation methodologies. MSI’s commitment to scientific excellence is reflected in its investment in scientific staff. Nearly half of MSI’s staff are Ph.D. scientists who are recognized experts in computational chemistry, biology, physics, and computer science. This scientific background is combined with expertise in software engineering and design. In-house experience is reinforced through close relationship with leading academic institutions, such as the California Institute of Technology, the University of California at Berkeley, Harvard University, and the University of Yale, Cambridge, and York.

Partnership and Services

Development, validation, and application of MSI products are conducted in close collaboration with users. A hallmark of this collaboration is MSI’s Consortia, application-focused groups of industrial researchers, leading academics, and MSI staff who develop strategies to solve problems in specific areas of industrial relevance. MSI sponsors Consortia in Catalysis and Sorption, Pharmaceutical Development, Polymers, Potential Energy Functions, and Combinatorial Chemistry.

About Pharmacopeia, Inc.

Pharmacopeia is a leader in drug discovery combining three platform technologies: informatics, small molecule combinatorial chemistry, and high-throughput screening. Through its wholly-owned subsidiary, Molecular Simulations Inc. (MSI), Pharmacopeia develops and commercializes molecular modeling, simulation, and informatics software and services. Using ECLiPS, its proprietary combinatorial chemistry technology, Pharmacopeia has generated more than 4.2 million diverse, easily identifiable, small molecules. Pharmacopeia tests these molecules using state-of-the-art high-throughput screening. These technologies are integrated to support the following businesses:

1) selling predictive modeling, information management, and structure-based design software to the life and materials science marketplace,

2) licensing collections of compounds to pharmaceutical companies for evaluation in multiple drug discovery programs,

3) identifying and optimizing lead compounds for specific targets provided by customers, and

4) licensing drug development candidates developed in Pharmacopeia’s internal drug discovery programs to pharmaceutical companies.


9685 Scranton Road
San Diego
United States of America


Phone: 619 458 9990
Fax: 619 458 0136

News Articles [514 Associated News Articles listed on BioPortfolio]

Atomic-Scale Simulations Test Metal Strength

NewsThe same simulations strongly suggest that the metal cannot be strengthened forever.Contributed Author: 

Supramolecular heterostructures formed by sequential epitaxial deposition of two-dimensional hydrogen-bonded arrays

Supramolecular heterostructures have been formed by the sequential deposition of two molecular layers with different symmetries and lattice constants — one consisting of carboxylic acid, the other o...

Probing the limits of metal plasticity with molecular dynamics simulations

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations—line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocat...

Neural networks carry out chemical simulations in record time

Researchers at the Universities of Vienna and Göttingen have succeeded in developing a method for predicting molecular infrared spectra based on artificial intelligence. These chemical "fingerprints"...

Simulations signal early success for fractal-based retinal implants

(University of Oregon) Computer simulations of electrical charges sent to retinal implants based on fractal geometry have University of Oregon researchers moving forward with their eyes focused on bio...

Physicists use computer simulations to study arrangement of stiff polymers in spherical cavities

Theoretical physicists led by Professor Kurt Binder and Dr. Arash Nikoubashman at Johannes Gutenberg University Mainz in Germany have used computer simulations to study the arrangement of stiff polyme...

Flu simulations suggest pandemics more likely in spring, early summer

(PLOS) New statistical simulations suggest that Northern Hemisphere flu pandemics are most likely to emerge in late spring or early summer at the tail end of the normal flu season, according to a new ...

Vical Incorporated Announces Pricing of $25 Million Underwritten Public Offering of Common Stock

SAN DIEGO, Nov. 08, 2017 (GLOBE NEWSWIRE) -- Vical Incorporated (Nasdaq:VICL) today announced the pricing of its underwritten public offering of 14,285,714 shares of common stock or common stock ...

PubMed Articles [1660 Associated PubMed Articles listed on BioPortfolio]

Assessing Statistical Uncertainties of Rare Events in Reactive Molecular Dynamics Simulations.

Reactive molecular dynamics (MD) simulations are a versatile tool which allow for studying reaction pathways and rates simultaneously. However, most reactions will be observed only a few times in such...

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations.

p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is hig...

Variable Regions of Antibodies and T-cell Receptors may not be Sufficient in Molecular Simulations Investigating Binding.

Antibodies and T-cell receptors are important proteins of the immune system that share similar structures. Both contain variable and constant regions. Insight into the dynamics of their binding can be...

Consistent principal component modes from molecular dynamics simulations of proteins.

Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use the technique has...

Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations.

ADP-ribosylhydrolases (ARH1, ARH2 and ARH3) are a family of enzymes to catalyze ADP-ribosylation, a reversible and covalent post-translational modification (PTM). There are four phosphorylated sites (...

Clinical Trials [1128 Associated Clinical Trials listed on BioPortfolio]

Improving Team Training During Mock Code Blue Simulations

Communication and teamwork failures are the leading causes of errors in healthcare settings. In situ mock code simulations are a potential means to train team-based skills using simulatio...

The Application of Ticagrelor Combined With Low Molecular Weight Heparin During PCI

The purpose of this study is to determine ticagrelor combining with low molecular weight heparin is effective and safe during PCI or not.

In Vivo EGFR Molecular Classification

The investigators developed 18F-MPG as a targeted molecular imaging agent for noninvasive and repeatable detecting EGFR-activating mutational status.

Clinical Value of Molecular Genetic Analyzes in Gynecological Malignomas

The aim of the planned research project is to find out the clinical significance of molecular genetic analyzes in gynecological malignomas. In particular, it will be investigated how the k...

Investigation of the Role of Hemodynamics in Re-stenosis of CABG Patients

CFD simulations in this study provide detailed hemodynamics information, which cannot be obtained from cardiac images alone. We hypothesize that our proposed simulations will provide stron...

Companies [879 Associated Companies listed on BioPortfolio]

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EPS serves the needs of emergency response organizations by helping them prepare for, respond to, and recover from emergencies.We do this through a unique program of thought provoking action based tra...


Founded in 2003, Kognito is a leader in immersive learning experiences that drive positive change in health behaviors. Kognito’s award-winning online and mobile simulations w...

Chemical Computing Group Inc.

CCG ( is a leading supplier of software solutions for Life Sciences. CCG’s drug discovery software platform is the Molecular Operating Environment (MO...


PRAECIS PHARMACEUTICALS INCORPORATED is a biopharmaceutical company focused on the discovery and development of novel compounds to address unmet medical needs or improve existing therapies.PRAECIS has...

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