JChemExtensions

* The current "JChem Extensions" is Version 1.3.5 (Oct 7th, 2008).
* These nodes may not include all function of original tools. Please contact us or refer brochure.
* In using JChem Extensions, user needs formal license of ChemAxon separately.
　

Details of JChem Extensions Nodes

Option
Database Extension
These nodes connect to the relational database from the Knime platform
	JChemCartridge Connecting to JChemCartridge for Oracle, it is available for the structure search (substructure, exact match and similarity). Searching is carried out in Oracle.
	JChemManager It is possible to connect to relational database by JDBC from Knime. (MS Access, MySQL, etc.)
	JChemSearch The structure search can be carried out through the relational database with JChemManager. The searching is on Knime.
	JChemUpdata It is possible to upload structures into relational database (MySQL, MS Access, etc.)
Manipulator Extension
A variety of ChemAxon's tools can be executed on the Knime platform.
	Charge【Calculator Plugins/ Charge】 The partial charge distribution determines many physico-chemical properties of a molecule, such as ionization constants, reactivity and pharmacophore pattern. Use Charge node to compute the partial charge value of each atom. Total charge is calculated from sigma and pi charge components, and any of these three charge values can be displayed.
	Orbital Electronegativity【Calculator Plugins/ Charge】 Partial charge distribution of the molecule is governed by the orbital electronegativity of the atoms contained in the molecule.
	Polarizabillity　【Calculator Plugins/ Charge】 The electric field generated by partial charges of a molecule spread through intermolecular cavities and the solvent. The induced partial charge (induced dipole) has a tendency to diminish the external electric field. This phenomenon is called polarizability. The more stable the ionized site is the more its vicinity is polarizable. This is why atomic polarizability is an important factor in the determination of pKa and why it is considered in our pKa calculation node. Atomic polarizability is altered by partial charges of atoms. Our calculation is based on Miller's and Savchik's paper, and takes into account the effect of partial charge upon atomic polarizability.
	Geometry　【Calculator Plugins/ Geometry】 The Geometry node provides characteristic values related to the geometrical structure of a molecule. It can calculate steric hindrance and Dreiding energy. The calculation can predict and use the lowest energy conformer of the input structure.
	Molecular Surface Area　【Calculator Plugins/ Geometry】 There are two types of available molecular surface area calculations, van der Waals and solvent accessible. Calculation method is based on the publication of Ferrara et al.
	Polar Surface Area　【Calculator Plugins/ Geometry】 Polar surface area (PSA) is formed by polar atoms of a molecule. It is a descriptor that shows good correlation with passive molecular transport through membranes, and so allows estimation of transport properties of drugs.
	Topology Analysis　【Calculator Plugins/ Geometry】 The Topology Analysis node provides characteristic values related to the topological structure of a molecule.
	H Bond Donor/ Acceptor　【Calculator Plugins/ Other】 Hydrogen Bond Donor-Acceptor calculates atomic hydrogen bond donor and acceptor inclination. Atomic data and overall hydrogen bond donor and acceptor multiplicity are displayed for the input molecule (or its microspecies at a given pH).
	Huckel Analysis　【Calculator Plugins/ Other】 Localization energies L(+) and L(-) for electrophilic and nucleophilic attack at an aromatic center are calculated by the Hückel method. The smaller L(+) or L(-) means more reactive atomic location. Order of atoms in E(+) or in Nu(-) attack are adjusted according to their localization energies. The total pi energy, the pi electron density and the total electron density are also calculated by the Hückel method. Depending on the chemical environment the following atoms have optimal Coulomb and resonance integral parameters: B, C, N, O, S, F, Cl, Br, I. All other atoms have a default, not optimized parameter. Theoretical background is taken from Isaacs' book. Additional literature for the Hückel's parameters is Streitwieser's book.
	Refractivity　【Calculator Plugins/ Other】 Our calculation is based on the atomic method proposed by Viswanadhan et al. Molar refractivity is strongly related to the volume of the molecules and to London dispersive forces that has important effect in drug-receptor interaction.
	LogD【Calculator Plugins/ Partitioning】 Calculate "logD" using ChemAxon Plugins. Compounds having ionizable groups exist in solution as a mixture of different ionic forms. The ionization of those groups, thus the ratio of the ionic forms depends on the pH. Since logP describes the hydrophobicity of one form only, the apparent logP value can be different. The octanol-water distribution coefficient, logD represents the compounds at any pH value.
	LogP【Calculator Plugins/ Partitioning】 Calculate "logP" using ChemAxon Plugins. The logP node calculates the octanol/water partition coefficient, which is used in QSAR analysis and rational drug design as a measure of molecular hydrophobicity. The calculation method is based on the publication of Viswanadhan et al. The logP value of a molecule is composed of the increment values of its atoms. The algorithm described in the paper was modified at several points. Many atomic types were redefined to accommodate electron delocalization. Contributions of ionic forms were added. The logP value of zwitterions are calculated from the logD value at the isoelectric point. The effect of hydrogen bonds on logP is considered if there is a chance to form a six membered ring between suitable donor and acceptor atoms. New atom types were introduced especially for sulfur, carbon, nitrogen, and metal atoms.
	IsoelectricPoint【Calculator Plugins/ Protonation】 Calculate "IsoelectricPoint" using ChemAxon Plugins. Net charge of an ionizable molecule is zero at a certain pH. This pH is called the isoelectric point, also referred to as pI.
	MajorMicrospecies【Calculator Plugins/ Protonation】 Calculate "MajorMicrospecies" using ChemAxon Plugins. Determines the major protonation form at a specified pH.
	pKa【Calculator Plugins/ Protonation】 Calculate "pKa" using ChemAxon Plugins. Most molecules contain some specific functional groups likely to lose or gain proton under specific circumstances. Each ionization equilibrium between the protonated and deprotonated forms of the molecule can be described with a constant value called pKa. The pKa node calculates the pKa values of all proton gaining or losing atoms on the basis of the partial charge distribution.
	BCUT 【Calculator Plugins】 Calculates lowest and highest eigenvalues of the original Burden matrix and the three variant introduced by Pearlamn and Smith (ref: R. S. Pearlman and K.M. Smith: Novel Software Tools for Chemical Diversity, Perspectives in Drug Discovery and Design, 9/10/11: 339-353, 1998.) These three variants are: atom charge, atom polarizability and hydrogen bond acceptor/donor properties. The number of lowest and/or highest eigenvalues to be calculated are specified in the corresponding parameter configuration.
	Chemical Fingerprint 【Calculator Plugins】 The fingerprints encode the topological connection between atoms of the chemical graph. Though such encoding loses information, still it preserves enough to allow fast comparisons of chemical structures without their direct structural comparison but instead involving their topological fingerprints.
	Elemental Analysis 【Calculator Plugins】 Calculate elemental properties using ChemAxon Plugins （Mass, Exact Mass, Formula, Isotope formula, Dot-disconnect formula, Composition, Isotope compositionAtomCount）
	IUPAC Name 【Calculator Plugins】 Generate "IUPAC Name" using ChemAxon Plugins
	ChemicalTerms Calculate some properties using ChemAxon Plugins. The combination of two or more expressions is possible.
	Fragmenter Fragmenter cleaves single bonds to generate molecular fragments. The cleavage rules correspond to chemical reactions in order to enhance synthetic accessibility. The cleavage points on the fragments are labeled with the cleavage rules.
	LibraryMCS LibraryMCS computes the maximum common substructure (MCS) of a set of compounds.
	MolSearch The substructure search on Knime platform
	R-Group Decomposition R-group decomposition is a special kind of substructure search that aims at finding a central structure - scaffold - and identify its ligands at certain attachment positions. The query molecule consists of the scaffold and ligand attachment points represented by R-groups.
	Standardizer Standardizer is a structure canonicalization tool in JChem for converting molecules from different sources into standard representational forms. Standardizer can automate the identification of mesomers and tautomers and can be used for counter-ion removal.

System requirement

Evaluation version and free academic package

How to get

Download : Evaluation version

We are ready for the evaluation version for customer's considering the purchase of it.
After downloading the program, you need to inquire the evaluation license code by e-mail. Please send us the following information. After confirmation of those information, we will send you the evaluation license which you can use JChem Extensions for two months maximally.

info-science@infocom.co.jp
Chem & Bio Informatics Department
Infocom Corporation

1. First Name/ Last Name
2. Job title
3. Department
4. Company or Organization
5. Address
6. E-mail address (* You need E-mail address which includes a domain of your organization.)

* If you are an academic customer, please refer to the information below.
* If you have any questions, don't hesitate to let us know.

JChem Extensions: Academic package (JChem Extensions: Base)

Academic customer can use the "JChem Extensions" free of charge.
Please see the page of "Academic package" for JChem Extensions.

Base
Converter Extension
These nodes convert "Molecule Data Type" between JChemExtensions and the third parties (e.g. Schrodinger, CDK, etc).It’s necessary to convert to “Molecule Data Type" which the third parties can recognize when user pass the structure information to the nodes of third party from JChemExtensions. And vice versa. Each third party defines its "Molecule Data Type” which recognizes the structure information on the KNIME platform. The "Molecule Data Type" of JChemExtensions is "MrvCell"
	MrvConverter Convert "Molecule Data Type" of the third parties to "MrvCell" which JChemExtensions recognize.
	MrvToMol2Converter Convert "Molecule Data Type" of JChemExtensions to "Mol2Cell" for the third parties which recognize "mol2" format.;
	MrvToPdbConverter Convert "Molecule Data Type" of JChemExtensions to "PdbCell" for the third parties which recognize "PDB" format.
	MrvToSdfConverter Convert "Molecule Data Type" of JChemExtensions to "SdfCell" for the third parties which recognize "SD" or "SDF" format.
	MrvToSmilesConverter Convert "Molecule Data Type" of JChemExtensions to "SmilesCell" for the third parties which recognize "SMILES" format.
	MrvToStringConverter Convert "Molecule Data Type" of JChemExtensions to "StringCell" for the third parties which recognize "string" format.

IO Extension
These nodes are for input and output of the structures on the KNIME platform. Whereas the nodes in Converter convert "Molecule Data Type" between the third parties and JChem Extensions, the MolImporter and MolExporter in IO can import/export the structure file (SDF, SMILES.etc..) directly. It is also possible to sketch structures on the Knime even if you have no structure file.
	MarvinSketch Chemical editor for drawing chemical structures, queries and reactions. Allow to sketch molecular structure in the dialog. Upon execute, the structure is available in the output table. "Molecule Data Type" defines "MrvCell".
	MolExporter The output file format can be specified as an argument with this node. Many different output file formats are supported "mol", "sdf", "smiles", "png", "jpeg", etc.
	MolImporter The input file format is guessed automatically. Many different formats are supported like "mol", "rgf", "sdf", "rdf", ", "mrv", "smiles", "pdb", "xyz". MolImporter can also import gzip compressed and base64 encoded structures.
	MultipleMolImporter It is possible to import two or more structural files at the same time. Supported formats are the same as MolImporter.
	PdbImporter Imports biochemical data from PDB file. Complex information defined by the PDB file is maintained. MolImporter can also import PDB file, but it does not recognize complex information.
Visualizer Extension
These nodes achieve high-quality structural visualization by using ChemAxon's tool on the Knime platform.
	MarvinSpace Using MarvinSpace you can visualize small molecules, proteins, nucleic acids, crystals, various molecular surfaces, molecular orbitals as well as volumetric data such as electrostatic potential, hydrophobicity. Manual overlay of structures and manual change of internal coordinates are also available.
	MarvinTable Load multiple molecules from a data and displays them in a regular two-dimensional tables of cells.
	MarvinView Load multiple molecules from a data and displays them in a scrollable viewer.

JChem Extensions contains about 40 novel nodes for the KNIME workflow platform, from basic functions dealing with chemical structure data to special functions using ChemAxon’s software tools such as Marvin, JChem, Standardizer and more.

For academic customer, INFOCOM offers “JChem Extensions” without charge.

Screenshots

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