Historic development of chemical notations

Wiswesser, William J.

doi:10.1021/ci00047a023

Cited by 51 publications

(33 citation statements)

References 29 publications

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“…To tackle this problem, he described a procedure for reducing the number of iterative mappings that must be performed by using certain guiding information of reactant–product atom equivalences. The latter can be conveniently obtained by comparison of the Wiswesser Linear Notation, symbol strings of the reacting molecules. This suggestion has led to the development of other faster but approximate approaches for the detection of reaction centers (see ‘ EC‐Based Methods ’).…”

Section: Common Substructure‐based Methodsmentioning

confidence: 99%

Automatic reaction mapping and reaction center detection

Chen¹,

Chen

Taylor³

2013

WIREs Comput Mol Sci

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A reaction center is the part of a chemical reaction that undergoes changes, the heart of the chemical reaction. The reaction atom–atom mapping indicates which reactant atom becomes which product atom during the reaction. Automatic reaction mapping and reaction center detection are of great importance in many applications, such as developing chemical and biochemical reaction databases and studying reaction mechanisms. Traditional reaction mapping algorithms are either based on extended‐connectivity or maximum common substructure (MCS) algorithms. With the development of several biochemical reaction databases (such as KEGG database) and increasing interest in studying metabolic pathways in recent years, several novel reaction mapping algorithms have been developed to serve the new needs. Most of the new algorithms are optimization based, designed to find optimal mappings with the minimum number of broken and formed bonds. Some algorithms also incorporate the chemical knowledge into the searching process in the form of bond weights. Some new algorithms showed better accuracy and performance than the MCS‐based method. WIREs Comput Mol Sci 2013, 3:560–593. doi: 10.1002/wcms.1140 This article is categorized under: Computer and Information Science > Chemoinformatics

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Section: Common Substructure‐based Methodsmentioning

confidence: 99%

Automatic reaction mapping and reaction center detection

Chen¹,

Chen

Taylor³

2013

WIREs Comput Mol Sci

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“…This subset uses only the symbols H, C, N, 0, P, S, F, C1, Br, I, and (,) and digits, with the following four rules: (1) Atoms are represented by atomic symbols. Although SMILES allows direct specification of charges, attached hydrogens, and aromaticity, often they are not required.…”

Section: Basic Smilesmentioning

confidence: 99%

SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

Weininger¹

1988

J. Chem. Inf. Comput. Sci.

5,486

3,859

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“…Development and efficient use of ligand data bases require universally applicable methods for the virtual representation of small molecules. SMILES (Simplified Molecular Input Line System) (Wiswesser, 1985) was developed as an unambiguous and reproducible method for computationally representing molecules. It was developed as an improvement over the Wiswesser Line Notation (Wiswesser, 1954), which had a cumbersome set of rules, but was a preferred method due to the representation of molecular structure as a linear string of symbols that could be efficiently read and stored by computer systems.…”

Section: B Ligand Databases For Computer-aided Drug Designmentioning

confidence: 99%