Computational Chemistry
The experience acquired over the years, experience documented by publications in international journals and participation to several national and international conferences, allows us to cope with professionalism and efficiency to any kind of chemoinformatics or bioinformatics problem. Scientia Advice di Roberto Artali offers a wide range of services, serving as a reliable and efficient partner in all phases of the research and development work. Our R&D platform is based on a relational database, the Scientia Advice Relational Database Management System (SA-RDBMS), and an integrated system of proprietary and Open Source tools, the Scientia Advice Molecular Modeling Workbench (SA-MMW), able to effectively access and process the information contained in the SA-RDBMS.
- The SA-RDBMS is based on the Powerful and Open Source object-relational database system PostgreSQL, and has been specifically created to allow the efficient storage and the treatment of chemical, physical-chemical, biochemical and toxicological data from millions of compounds of natural and synthetic origin, derived from the scientific literature and my personal research and collaborations in various areas of chemistry, biochemistry and medicinal chemistry.
- The database is fully managed by the integrated system SA-MMW, a set of tools specifically developed to allow to process as efficiently as possible the great amounts of data stored in the SA-RDBMS database. The system consists of a set of FORTRAN routines (optimized to run on parallel and vector architectures to achieve the highest possible efficiency) and controlled by Python scripts, providing at the same time a simple, safe and easily modifiable interface to the database system.
The applications of this integrated system to computational chemistry and molecular modeling include:
- Conformational analysis and optimization of molecular structures using different levels of abstraction (molecular mechanics, molecular dynamics, semi-empirical quantum chemistry, ab initio quantum chemistry and QMMM mixed methods).
- Physicochemical properties predictions (steric, electronic) and molecular descriptors calculation for QSAR and QSPR applications.
- (eco)toxicity and ADMET profiles predictions.
- Theoretical studies of chemical reactions and elucidation of the reaction mechanisms to improve the reaction yields.
- Chemometrics, processing, storage and sharing of analytical and spectral data. Multivariate data analysis and classification.
- Critical evaluation of the theoretical results.
The core of the whole bioinformatics system is represented by the molecular docking routines, designed to predict the interaction energies of ligands contained in the SA-RDBMS database vs. hundreds of different targets (receptors, enzymes, proteins, DNA fragments, integral membrane models,...) categorized and stored according to their biological and biochemical properties. Starting from a detailed analysis of the problem our system represents a unique and multidisciplinary solution to support, address and accelerate any project whose objective is to find the best therapeutic target for a particular chemical or the proper drug for a particular therapeutic target.
Our expertise is at your service to choose the best method and the best suited software solution to carry out specific parts of a research project:
- Homology modeling of proteins, membrane receptors and enzyme systems.
- Building and validation of three-dimensional models of enzymatic systems, nucleic acids and integral membrane systems containing one or more proteins and/or receptors.
- Classical and multi-target Molecular docking and virtual screening.
- Theoretical studies of the drugs-proteins, drugs-DNA and drugs-membrane interactions.
- Nanomaterials model building and their interaction with the biological systems.