ChemSpace3D

Molecular Modeling Toolkit

A Blue Cube Project

ChemSpace3D


< IS NOT >

  • a molecular 3D-viewer - graphics and visualisation abilities are on the one hand improved permanently, but on the other hand this is not the primary goal of the development process
  • incredible fast, because it's implemented 'from scratch' in C# using the MS .Net framework and the associated GDI+ , so it neither relies on pre-assembled code of other computational chemistry environments, nore uses a graphical 3D-engine


< IS >

  • first of all a computational, molecular modeling tool, providing a couple of features in a synergetic combination - hopefully
  • intended to develop into an open system for chemists (especially students), dealing with molecular mechanics, and providing basic functionality embedded into a modern concept of software design and development 

The Author


In August 1994 Udo P. Ottmann graduated in the field of computational chemistry at the chair of Prof. Ivar K. Ugi (Technical University of Munich). Against the usual procedure, he did not continue with a thesis in chemistry, but went into the field of technical software development, highly specialized in OOA, OOD and simulation software (e.g. SIEMENS/Sitras SidyTrac - physical & electrical train movement simulator). For one year (2002-2003) he then followed the scientific team of Prof. Johann Gasteiger at the CCC,  Friedrich-Alexander-University located in Erlangen/Germany. After a another period of technical software development, he finally turned back to chemistry/chemoinformatics, joining a chemical startup company in Munich, highly specialized in multi component reactions (MCR) - and in close cooperation with Boehringer Ingelheim - where he set up a new section for chemoinformatics, computationally supporting the power of MCR-chemistry applied to develop a novel active compound against cancer, by implementing specific software-tools in the fields of Molecular Modeling, Conformational Search, Docking, Combinatorial Chemistry, 2D/3D-Similarity Search and Molecular 2D/3D-Descriptors. During this phase he was assisted and trained by Dr. Lutz Weber (OntoChem GmbH, Halle/Germany), a great mentor and medicinal chemist. For another 3 years (2013-2016) he then supported the german company FRANKENRASTER GmbH, dealing with digitalisation and archivation of documents of each kind, also setting up a specific software structure, designed for the special needs of the company. After a 'time out', based on illness, Udo is now again involved in chemoinformatics and theoretical chemistry as 'self-employed' computer scientist...


... but otherwise also an Unidentified Drumming Object ...

Projects


LATEST

  •  The Ring Closure Problem - An Approach... ...Leading to Novel Internal Molecular Coordinates, Describing the Conformational Space of Cyclic Flexible Molecules.

         ...SOLVED !!! ...a scientific publication is                 under progress...



CURRENT

  • Interface-Interaction Theory (I²T)

         ...basically it's very simple, but the                         consequences seem to be fundamental...               ...the exact mathematical formulation is                 under progress and consistent so far - it will           provide a nexus to analytical mechanics                 and statistical thermodynamics...


  • Xenesis - Evolutionary Simulation Engine for Systems Arising from Self-Organising Processes

         ...the central processing kernel works                     robust...


  • Chemesis - Simulation of Molecular Evolution by Processes of Self-Organisation based on the Xenesis Engine and the underlying I²T

         ...computer simulations provide the                         expected chemical results...


  • The "ABC-L" - A Self Defining Modeling and Programming Language Based on Human Associative Thinking... Inspired by the UML.

        ...preliminary studies performed...

        ...intended: the ABC-L as a programming               language for the Xenesis System,                      because both rely on the same                            fundamental principles


              • ChemSpace3D.Net / Evolution.Net - Software Components for Scientific Programmers using MS Visual Studio (C#, VB).

                       ...a lot of diligence work... Deffered !




              Features


              Conformational Search

              ...can optionally be performed as pure 'Random Walk' or via 'Evolutionary or Genetic Algorithm' optimization strategies. The latter are driven by the proprietary Evolution.NET engine, which can easily be adapted to every kind of optimization problem. Both, acyclic and cyclic molecular systems can be conformationally explored.

               


              Docking

              ...there are three modes of docking.

              • ligand is rigid => degrees of freedom f = 6
              • ligand is flexible => degrees of freedom f = 6 + N - 3
              • ligand is flexible, but fixed => degrees of freedom f = N - 3



              Cavity Finding

              ...the algorithm used to identify cavities (potential active sites) on protein surfaces is  protected by patent at the European Patent Office (EP2577530), but meanwhile also global via United States Patent (US20130184163).



              Desolvation and Hydrophobicity

              ...an additional, heuristic and entropic force-field term is available, taking into account the effects of desolvation and hydrophobicity, leading to a significant improvement of  results, when exploring the potential hypersurface of molecular interaction (e.g. docking).



              Similarity Search

              ...in R² and R³ will be available soon, using highly efficient descriptors of molecular structure, also protected by the aforementioned patent .

              Very Thanks To


              • "Ivar" (Prof. Ivar K. Ugi),  "God-Father" of computational chemistry

              for teaching me the fundamental relation between chemistry and mathematics

               

              • "Johnny" (Prof. Johann Gasteiger), "Jesus" of computational chemistry

              for teaching and training me, how to perform chemistry on the computer

               

              • "Eric" (Priv. Doz. Dr. Eric Fontain), Amazing creative computational chemist in the field of evolutionary algorithms (EA) applied to chemical optimization problems, e.g. the "protein folding problem"

              for teaching me, how to work scientifically in a correct way, and supporting me to follow my individual scientific intuitions


              • Prof. Dr. N. Rösch, Probably One of the Best Theoretical Chemists Ever and a Great Mathematican

              for taking away my fear from mathematics and teaching me, how to use it to solve chemical problems

               

              • Dr. Lutz Weber, Ingenious Medicinal Chemist and Computational Chemist

              for teaching me, how the whole process of drug design works

               

              for giving me the "chemical input" - my greatest team-player ever ("the dynamic duo")

               

              for teaching me, how to fight and never surrender, even we got to fight with ower own illness


              for teaching me, how to analyse, design and implement complex software-systems

               

              • Sabine Meier (my beloved wife), Intensive Nurse in the Field of Childhood Cancer and Maintaining the Life of Premature Infants.

              for medicinal discussions and her patience for endless nights of calculations and programming


              • Elke Riemer,  Scoolmaster in the Field of Chemistry and Biology

              for teaching me the basics of organic chemistry



              mail to: info@chemspace3d.xyz

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