Online Chemical e-Laboratory

ChemoSophia is a company specializing in software development and its online application for cheminformatics, bioinformatics, computational toxicology researches as well as physicochemical properties calculation. Our main customers are pharmaceutical, biotechnology and agrochemical companies, as well as academic research groups and environmental agencies integrating computations in their services and products as well as in environmental protection.

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ChemoSophia has received no funding and grants from any governmental, commercial organization, individual or investor. It performs free automatic computations in the area of chemistry and bioinformatics including modelling of structure, conformational analysis, estimation of electron, physical-chemical properties and bioactivities of molecules and complex systems.
We are sorry for incomplete visualization. The computations are time-consuming, requiring correct modelling of structure and reliable computations of molecular characteristics, parameters of interactions with receptors (energies, forces, force constants), electron characteristics. We did our software to help scientists in design of new perspective drugs and materials.

Software is based on the models of Dr. Vladimir Potemkin and Dr. Maria Grishina.

We hope that the software will contribute in making people healthier and the world better.

To cite us, please use the following references:

Electron properties based on AlteQ method and AlteQ method itself:
1. Maria Grishina, Oleg Bolshakov, Andrey Potemkin, Vladimir Potemkin. Theoretical investigation of electron structure and surface morphology of titanium dioxide anatase nano-particles //Computational and Theoretical Chemistry (2016), Vol. 1091, September, pp. 122-136 DOI information: 10.1016/j.comptc.2016.07.003

2. Potemkin V.A., Grishina M.A. A new paradigm for pattern recognition of drugs// J. Comput. Aided Mol. Des.- 2008.- V. 22.- P. 489 - 505.

Prognosis of bioactivities, molecular docking, drug discovery and design methods:
1. Potemkin V.A., Grishina M.A. A new paradigm for pattern recognition of drugs// J. Comput. Aided Mol. Des.- 2008.- V. 22.- P. 489 - 505.
2. Potemkin V., Grishina M. Principles for 3D/4D QSAR classification of drugs// Drug Discovery Today.- 2008.- V. 13.- No. 21/22.- P. 952 - 959.
3. Potemkin V, Pogrebnoy A., Grishina M. A Technique for Energy Decomposition in the Study of "Receptor-Ligand" Complexes //Journal of Chemical Information and Modeling - 2009.- Vol. 49.- N 6.- P. 1389 - 1406.
4. Potemkin V.A., Grishina M.A., Bartashevich E.V. Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework// Journal of Structural Chemistry - 2007.- V. 48.- No. 1.- P. 155 - 160.
5. Pereyaslavskaya E.S., Potemkin V.A., Grishina M.A., Bartashevich E.V. The analysis of pharmacophoric parts of DHFR - inhibitors using 3D-QSAR algorithm BiS/MC and X-ray data// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 87.
6. Grishina M.A., Bartashevich E.V., Pereyaslavskaya E.S. and Potemkin V.A. A Novel Techniques for Virtual Discovery for Study of Multistage Bioprocesses// Drugs of the Future.- 2007.- Vol. 32, Suppl. A.- P. 27.

Multiconformational analysis (4D molecular model) is based on the AlteQ energy estimation with the search of conformers presented in:
1. Potemkin V.A., Arslambekov R.M., Bartashevich E.V., Grishina M.A., Belik A.V., Perspicace S. and Guccione S. Multiconformational Method for Analyzing the Biological Activity of Molecular Structures// J. Struct. Chem.- 2002.- V.43.- N 6.- P. 1045 - 1049.

Physicochemical properties estimation is based on MERA (ChemoSophia Elastic model):
1. Potemkin V, Pogrebnoy A., Grishina M. A Technique for Energy Decomposition in the Study of "Receptor-Ligand" Complexes //Journal of Chemical Information and Modeling - 2009.- Vol. 49.- N 6.- P. 1389 - 1406.
2. Bartashevich E.V., Potemkin V.A., Grishina M.A. and Belik A.V. A Method for Multiconformational Modeling of the Three Dimensional Shape of a Molecule// Journal of Structural Chemistry. - 2002.- V43. - N. 6.- P. 1033 - 1039.

Modelling of many-particle systems is presented in:
1. Grishina M.A., Bartashevich E.V., Potemkin V.A. and Belik A.V. Genetic Algorithm for Predicting Structures and Properties of Molecular Aggregates in Organic Substances// Journal of Structural Chemistry - 2002. - V.43.- N6.- P. 1040 - 1044.

Patents:

1. Maria Grishina and Vladimir Potemkin, BiS/MC (multi-conformational), registered in the SoftWare list 18 February 2008, call N 2007613594 issued 7 September 2007

2. Maria Grishina and Vladimir Potemkin, ProK N2008610190, registered in the SoftWare list 9 January 2008, call N 2007613591 issued 7 September 2007

3. Maria Grishina and Vladimir Potemkin, GonGO N 2007614593 registered in the SoftWare list 31 October 2007, call N 2007613592 issued 7 September 2007

Full list of publications see here .

 
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