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About Molsoft L.L.C.

Company History | ICM History

Welcome to Molsoft LLC! Molsoft is 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.

Some of the participants at the 2018 ICM User Group Meeting after lunch at Del Mar beach

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

MolSoft is building unique technologies for structure prediction that improves our understanding of the spatial organization of biological molecules and their interactions with each other, their biological substrates and drug-like molecules at the atomic level. Application of these rules and algorithms to specific biomedical problems allows us to address the following problems:

  • Molecule visualizing and data sharing
  • 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
  • Enterprise-wide cheminformatic databases.

Company History

Molsoft company was founded in 1994 by Ruben 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. MolSoft has 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.

Molsoft moved from New Jersey to La Jolla, California in 1999. From 1999 to 2010 we were located near the Pacific Ocean next to the Scripps Research Institute. In November 2010 we moved to custom built and designed offices in Sorrento Valley not too far from our previous home.

Brief History of ICM

by MolSoft's founder Ruben Abagyan Ph.D.
Ruben Abagyan Max Totrov Eugene Raush

The first lines of ICM were born in 1985 out of a desire to design a fast yet general framework for predicting the structure of complex biological macromolecules and their complexes. I formulated a set of requirements for a program for molecular mechanics in a full set of internal coordinates, and started working on the internal coordinate algorithms and the Fortran code of the first program blocks. By 1991 the batch parameter files were replaced by a command language and an interactive shell that looked quite similar to the current version of ICM; the molecules started to follow commands and sample the energy minima.

Max Totrov and I extended or rewrote most parts of ICM from 1991 to 1994. By 1993 several people (Alexey Mazur, Mikhail Petukhov, and Dmitry Kuznetsov) had also contributed to the fortran version of ICM, however their contributions did not survive in the current version of the program. Alexey pursued the development of molecular dynamics in internal coordinates which was first formulated and tested in a series of papers in 1989 and, later, branched out of ICM.

The all-C version of ICM emerged in 1994 as a result of a full rewrite. Some features were lost, but more were gained. Serge Batalov joined the development of the program in the fall of 1994, about the time Molsoft was founded. Another contributor to the code was Levon Budagyan.

Eugene Raush is writing the graphics user interface, chemical functions and pretty much anything else. The three of us work together to keep ICM strong, clean, healthy and alive.

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