About Molsoft L.L.C.

Company History | ICM History

Welcome to MolSoft LLC! MolSoft is a leading provider of innovative softwar and expert consulting services in structure prediction, structural proteomics, bioinformatics, cheminformatics, and drug discovery and design. We offer fully customized solutions tailored to the needs of biotechnology and pharmaceutical companies, addressing challenges in computational biology and chemistry. At MolSoft, we are dedicated to continuous innovation, scientific excellence, and the development of cutting-edge technologies and original ideas, driving advancements in the life sciences.

MolSoft provides innovative software tools and comprehensive services for drug discovery, molecular modeling, cheminformatics, bioinformatics, and corporate data management. We also form strategic partnerships with biotechnology and pharmaceutical companies to advance cutting-edge research and development.

MolSoft is pioneering unique technologies for structure prediction that enhance our understanding of the spatial organization of biological molecules and their interactions with one another, their biological substrates, and drug-like molecules at the atomic level. By applying these sophisticated algorithms and rules to biomedical challenges, we address a wide array of scientific problems, including:

• Visualizing molecules and sharing data seamlessly.
• Building and validating structural models of protein targets.
• Identifying biological ligand binding sites and novel allosteric regulatory sites on proteins of interest.
• Evaluating and ranking drug targets, including protein-protein interaction interfaces, to design strategies for rational drug development.
• Screening virtual libraries containing millions of compounds using MolSoft's revolutionary flexible docking and scoring procedures.
• Identifying interaction hot spots, such as key amino-acid positions involved in protein-protein interactions.
• Predicting protein loop conformations with high accuracy.
• Designing proteins with tailored properties for specific applications.
• Docking flexible peptides to protein targets and designing peptides that block protein-protein interactions.
• Converting 2D molecular structures to 3D, performing analysis, and clustering ultra-large compound libraries.
• Predicting compound properties, building QSAR models, and constructing and searching 3D pharmacophores.
• Creating and managing enterprise-wide cheminformatics 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.