About Molsoft L.L.C.

Welcome to Molsoft LLC! Molsoft a leading provider of tools, databases and consulting services in the area of structure prediction, structural proteomics, bioinformatics, cheminformatics, molecular visualization and animation, and rational drug design. Molsoft offers complete solutions customized for a biotechnology or pharmaceutical company in the areas of computational biology and chemistry. Molsoft is committed to continuous innovation, scientific excellence, the development of the cutting edge technologies and original ideas.

Molsoft offers software tools and services in lead discovery, modeling, cheminformatics, bioinformatics, and corporate data management; and forms partnerships with biotechnology and pharmaceutical companies.

For many years Molsoft is building unique technologies for structure prediction and is increasing our understanding of spatial organization of biological molecules and their interactions with each other, their biological substrates and drug-like molecules at atomic level. Application of these rules and algorithms to specific biomedical problems may allow us to address the following problems:

Building and validating structural models of protein targets
Identifying biological ligand binding sites or new sites for allosteric regulation of a protein of interest.
Evaluating and ranking drug targets, including protein-protein interaction interfaces, designing strategies for rational drug design
Screening virtual libraries of millions of compounds using the revolutionary Molsoft flexible docking and scoring procedure.
Identifying interaction hot-spots, i.e. the candidate amino-acid positions involved in protein-protein interactions
Predicting loop conformations in proteins
Designing proteins with desired properties
Docking flexible peptides to proteins
Designing peptides blocking protein-protein interactions
2D to 3D conversion, analysis and clustering of large compound libraries,
Predicting compound properties, building QSAR models, 3D pharmacophore construction and search

Company History

Molsoft company was founded in 1994 by Ruben and Margarita Abagyan as Biosoft and was renamed in 1995 to Molsoft. The Molsoft molecular modeling technology is based on the Internal Coordinate Mechanics (ICM) approach which gives a general modeling and structure prediction framework for many tasks of structural biology and rational drug design. The ICM project was initiated by the founder in 1985, and is being continuously developed ever since. In 2000, Dr. Maxim Totrov who worked with Dr. Abagyan since 1991 joined Molsoft as Principal Scientist. In 2002, Eugene Raush joined the team as a Senior Software Engineer. A strong team of administrators, researchers and software developers, its dynamic and creative environment allows Molsoft to address the most challenging problems of computational proteomics and rational drug design.

The basic algorithms used in ICM make this software an ideal platform for peptide prediction,homology modeling and loop simulations, flexible macromolecular docking and refinement. Over time, the complexity of problems related to structure prediction and analysis, as well as the desire for perfection, compactness and consistency, have lead the program to expansion into neighboring areas such as graphics, chemistry, sequence analysis and database searches, mathematics, statistics and plotting.

Molsoft moved from New Jersey to La Jolla, California in 1999. It is located near Pacific Ocean next to the Scripps Research Institute.