Irredundant Generation of Isomeric Molecular Structures with Some Known Fragments

Molchanova, Marina S.; Зефиров, Н. С.

doi:10.1021/ci970015p

Cited by 13 publications

(16 citation statements)

References 38 publications

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“…The free CDK Descriptor GUI (v0.94) [23] is a software for molecular descriptor calculation and is based on the open source chemistry development kit [24]. The Kier and Hall descriptors (electrotopological E-state state indices) [25] were used on a dataset of all 13190 C 8 H 16 O 2 isomers generated with the SMOG2 isomer generator software [26]. The high-speed molecular formula calculator HR2 was downloaded from [27] and performed a generation of all 28,008,691 elemental compositions including the elements (C:1-78 H:1-126 N:0-20 O:0-27 P:0-9 S:0-14) below 1000 Da according to the Seven Golden Rules [28].…”

Section: Methodsmentioning

confidence: 99%

Software platform virtualization in chemistry research and university teaching

et al. 2009

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BackgroundModern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories.ResultsVirtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs.ConclusionSoftware virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.Electronic supplementary materialThe online version of this article (doi:10.1186/1758-2946-1-18) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Software platform virtualization in chemistry research and university teaching

et al. 2009

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“…The ‘badlist’ and ‘goodlist’ result from constraints deduced from experimental spectra, and the output is optimally limited to only a handful of possibilities from which the correct structure can be deduced. This approach became an entire field of research on its own known as computer‐assisted structure elucidation (CASE), and which uses various structure generators,36,37 such as MYCIN,38 MOLGEN,39 and CONGEN,40 as a key component 41–45. However, none of these programs have been used to generate large libraries as a tool to explore the contents of chemical space.…”

Section: The Enumeration Of Chemical Spacementioning

confidence: 99%

The enumeration of chemical space

Reymond¹,

Ruddigkeit²,

Blum³

et al. 2012

WIREs Comput Mol Sci

124

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In the field of medicinal chemistry, the chemical space describes the ensemble of all organic molecules to be considered when searching for new drugs (estimated >1060 molecules), as well as the property spaces in which these molecules are placed for the sake of describing them. Molecules can be enumerated computationally by the millions, which was first undertaken in the field of computer‐aided structure elucidation. Scoring the enumerated virtual libraries by virtual screening has recently become an attractive strategy to prioritize compounds for synthesis and testing. Enumeration methods include combinatorial linking of fragments, genetic algorithms based on cycles of enumeration and selection by ligand‐based or target‐based scoring functions, and exhaustive enumeration from first principles. The chemical space of molecules following simple rules of chemical stability and synthetic feasibility has been enumerated up to 13 atoms of C, N, O, Cl, S, forming the GDB‐13 database with 977 million structures. The database has been organized in a 42‐dimensional chemical space using molecular quantum numbers (MQN) as descriptors, which can be visualized by projection in two dimensions by principal component analysis, and searched within seconds using a Web browser available at www.gdb.unibe.ch. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Computer and Information Science > Chemoinformatics

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“…SAG "identification parameters" are specified as follows: active major value (AMV), total active value (TAV), inactive (8,8); (9,9);(10,10); (11,11); (12,12); (13,13); (14,14); (15,15); (16,16); (17,17); (18,18); (19,19); (20,20); (21,21); (22,23); (24,24); (25,25); (26,26); (27,27); (28,28) (10,17); (11,20); (12,19); (13,18); (14,15); …”

Section: Stereoisomer Generationmentioning

confidence: 99%

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

Contreras

Álvarez

Guajardo

et al. 2006

J. Chem. Inf. Model.

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Generation of organic stereoisomers with R/S, Z/E, and/or M/P configurations that may contain heteroatoms, multiple bonds, and any kind of cycle (isolated, spiro, condensed, and nested) is described. Inputs for processing are molecular structures in a N_tuple format resident on an automatic (canonical) or manual (non canonical) generated file which are processed by doing internal molecular graph construction, a weighted bipartite tree construction for all atoms and bonds to detect stereocenters, and symmetrical atom groups (SAG) with some specific SAG parameters that constitute a novel way for redundancy elimination of meso structures. Finally, determination of ligand CIP priorities allows for writing the output N_tuples with stereoisomer description. Several examples showing application of this methology to a wide number of structures are also presented.

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Irredundant Generation of Isomeric Molecular Structures with Some Known Fragments

Cited by 13 publications

References 38 publications

Software platform virtualization in chemistry research and university teaching

Software platform virtualization in chemistry research and university teaching

The enumeration of chemical space

Algorithm for Exhaustive and Nonredundant Organic Stereoisomer Generation

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