(CDK): an Open-Source Java Library for Chemo- and Bioinformatics
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Practical Chemoinformatics Muthukumarasamy Karthikeyan • Renu Vyas
Practical Chemoinformatics Muthukumarasamy Karthikeyan • Renu Vyas Practical Chemoinformatics 1 3 Muthukumarasamy Karthikeyan Renu Vyas Digital Information Resource Centre Scientist (DST) National Chemical Laboratory Division of Chemical Engineering and Pune Process Development India National Chemical Laboratory Pune India ISBN 978-81-322-1779-4 ISBN 978-81-322-1780-0 (eBook) DOI 10.1007/978-81-322-1780-0 Springer New Delhi Dordrecht Heidelberg London New York Library of Congress Control Number: 2014931501 © Springer India 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recita- tion, broadcasting, reproduction on microfilms or in any other physical way, and transmission or infor- mation storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar meth- odology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplica- tion of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publica- tion does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
JRC QSAR Model Database
JRC QSAR Model Database EURL ECVAM DataBase service on ALternative Methods to animal experimentation To promote the development and uptake of alternative and advanced methods in toxicology and biomedical sciences SDF - STRUCTURE DATA FORMAT: How to create from SMILES The European Commission’s science and knowledge service Joint Research Centre Directorate F Health, Consumers & Reference Materials Chemicals Safety & Alternative Methods Unit The European Commission’s science and knowledge service Joint Research Centre EUR 28708 EN This publication is a Tutorial by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide user support. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication. Contact information Email: [email protected] JRC Science Hub https://ec.europa.eu/jrc JRC107492 EUR 28708 EN PDF ISBN 978-92-79-71294-4 ISSN 1831-9424 doi:10.2760/952280 Print ISBN 978-92-79-71295-1 ISSN 1018-5593 doi:10.2760/668595 Luxembourg: Publications Office of the European Union, 2017 Ispra: European Commission, 2017 © European Union, 2017 The reuse of the document is authorised, provided the source is acknowledged and the original meaning or message of the texts are not distorted. The European Commission shall not be held liable for any consequences stemming from the reuse. How to cite this document: Triebe -
Designing Universal Chemical Markup (UCM) Through the Reusable Methodology Based on Analyzing Existing Related Formats
Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software s t tools and two stage analysis procedure that supplied the necessary information for the n i r development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, P CTfile and XDfile. In addition the following formats were included in the first stage only: e r P CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results: A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. -
MACSIMUS Manual
1 MACSIMUS manual benzocaine (ethylaminobenzoate) parameter_set = charmm21 HA | HA-CT-HA | HA-CT-HA | OSn.2 | Cp.7=On.5 | C6R--C6R-HA Most often used links: | | HA-C6R C6R-HA 2.2 Blend synopsis and options | | HA-C6R--C6R-NPn.5^-Hp.25 9.2 Cook synopsis and options | 9.2.5 Cook input data Hp.25 MACromolecule SIMUlation Software © Jiˇr´ıKolafa 1993{2020 MACSIMUS may be distributed under the terms of the GNU General Public Licence Credits: ray: Mark VandeWettering \reasonably intelligent raytracer" CHARMM force field (files: charmm*.par, charmm*/*.rsd) GROMOS force field (files: gromos*.par, gromos*/*.rsd) amoeba implementation by Z. Wagner moil support by J. Schofield several bug fixes by T. Trnka bug discovered by N. Parfenov Contents I Program `blend' version 2.4b 14 1 Introduction 16 1.1 Force fields...................................... 16 1.2 `blend' overview.................................... 16 1.3 Versions........................................ 17 2 Running blend 18 2.1 Environment...................................... 18 2.2 Synopsis........................................ 19 2.2.1 Global options................................. 19 2.2.2 par-options and parameter files....................... 20 2.2.3 mol-options and molecular files....................... 22 2.2.4 Extra-options ................................. 29 2.3 File extensions.................................... 34 2.4 Run-time control................................... 37 2.4.1 get data format for input........................... 37 2.4.2 Scrolling.................................... 38 2.4.3 Error handling................................ 39 2.4.4 Interrupts................................... 40 2.5 Showing molecules graphically............................ 40 2.5.1 X11 Graphics................................. 40 2.5.2 Playback output............................... 44 2.6 Energy minimization................................. 44 2.7 Missing coordinates.................................. 45 3 Force field and the parameter file 46 3.1 Structure of the parameter file........................... -
Ontology-Based Classification of Molecules
Ontology-Based Classification of Molecules: a Logic Programming Approach Despoina Magka Department of Computer Science, University of Oxford Wolfson Building, Parks Road, OX1 3QD, UK [email protected] Abstract. We describe a prototype that performs structure-based classification of molecular structures. The software we present implements a sound and com- plete reasoning procedure of a formalism that extends logic programming and builds upon the DLV deductive databases system. We capture a wide range of chemical classes that are not expressible with OWL-based formalisms such as cyclic molecules, saturated molecules and alkanes. In terms of performance, a no- ticeable improvement is observed in comparison with previous approaches. Our evaluation has discovered subsumptions that are missing from the the manually curated ChEBI ontology as well as discrepancies with respect to existing subclass relations. We illustrate thus the potential of an ontology language which is suit- able for the Life Sciences domain and exhibits an encouraging balance between expressive power and practical feasibility. Keywords: Knowledge representation and reasoning, Logic programming and answer set programming, Cheminformatics. 1 Introduction The volume of bioinformatics data produced by research laboratories worldwide is in- creasing at an astonishing rate turning the need to adequately catalogue, represent and index the vast amounts of Life Sciences data sources into a pressing challenge. Semantic technologies have achieved significant progress towards the federation of biochemical information [33, 3, 4] via the definition and use of domain vocabularies with formal semantics, also known as ontologies. OWL [15], a family of logic-based knowledge representation (KR) formalisms standardised by W3C, has played a pivotal role in the advent of Semantic technologies due to its significant ability to reason over ontolo- gies by means of logical inference. -
Chemical File Format Conversion Tools : a N Overview
International Journal of Engineering Research & Technology (IJERT) ISSN: 2278-0181 Vol. 3 Issue 2, February - 2014 Chemical File Format Conversion Tools : A n Overview Kavitha C. R Dr. T Mahalekshmi Research Scholar, Bharathiyar University Principal Dept of Computer Applications Sree Narayana Institute of Technology SNGIST Kollam, India Cochin, India Abstract— There are a lot of chemical data stored in large different chemical file formats. Three types of file format databases, repositories and other resources. These data are used conversion tools are discussed in section III. And the by different researchers in different applications in various areas conclusion is given in section IV followed by the references. of chemistry. Since these data are stored in several standard chemical file formats, there is a need for the inter-conversion of II. CHEMICAL FILE FORMATS chemical structures between different formats because all the formats are not supported by various software and tools used by A chemical is a collection of atoms bonded together the researchers. Therefore it becomes essential to convert one file in space. The structure of a chemical makes it unique and format to another. This paper reviews some of the chemical file gives it its physical and biological characteristics. This formats and also presents a few inter-conversion tools such as structure is represented in a variety of chemical file formats. Open Babel [1], Mol converter [2] and CncTranslate [3]. These formats are used to represent chemical structure records and its associated data fields. Some of the file Keywords— File format Conversion, Open Babel, mol formats are CML (Chemical Markup Language), SDF converter, CncTranslate, inter- conversion tools. -
JUMBO Is an Opensource Toolkit Addressing the Semantic and Ontological Impedances That Are Major Barriers to Interoperability in Computational Chemistry and Physics
a a c a b a a c d a b c d JUMBO is an OpenSource toolkit addressing the semantic and ontological impedances that are major barriers to interoperability in computational chemistry and physics. Users build XMLSchemas from generic XML components to support particular computational tasks, such as high-throughput chemistry. JUMBO components provide a complete semantic description of information to or from a code such as MOPAC or GAMESS. Codes are edited to use JUMBO libraries as adapters to program-independent XML objects, or output is transduced using a generic parser, JUMBOMarker. The JUMBO system is designed for flexible collaborative contributions. abstract and rely on dictionaries (v.i.) to add semantics and ontology. In practice many of the concepts in a program are not in the schema but Existing codes in quantum mechanics or provided by domain-specific dictionaries. crystal/molecular mechanics/dynamics rely on The ultimate goal is to provide simple and “FORTRAN-like” input and output with flexible tools to XMLise existing and future variable and misunderstandable semantics and computational codes so they can be used as ontology. Typical examples are the lack of “black-boxes” in eScience workflows. Some explicit scientific units or fuzziness over authors have adopted this approach and whether a molecule has a charge. It is difficult embedded calls to JUMBO libraries in their to chain the output of one program into the code for input and output. However in some input of the next so human “cut-and-paste” is cases native legacy methods must still be used frequent. JUMBO allows authors and users to (for example where we do not have access or wrap these codes in XML and convert them to permission to modify source). -
Optimizing the Use of Open-Source Software Applications in Drug
DDT • Volume 11, Number 3/4 • February 2006 REVIEWS TICS INFORMA Optimizing the use of open-source • software applications in drug discovery Reviews Werner J. Geldenhuys1, Kevin E. Gaasch2, Mark Watson2, David D. Allen1 and Cornelis J.Van der Schyf1,3 1Department of Pharmaceutical Sciences, School of Pharmacy,Texas Tech University Health Sciences Center, Amarillo,TX, USA 2West Texas A&M University, Canyon,TX, USA 3Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom, South Africa Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs. To bring a new drug to the market is very costly, with the current of combinatorial approaches and HTS. The addition of computer- price tag approximating US$800 million, according to data reported aided drug design technologies to the R&D approaches of a com- in a recent study [1]. Therefore, it is not surprising that pharma- pany, could lead to a reduction in the cost of drug design and ceutical companies are seeking ways to optimize costs associated development by up to 50% [6,7]. -
E:\Projekty\2001\Bulletin\2001\No07\Buletin 2001 7.Vp
Chemický průmysl ČR 2000 – Myslet globálně, jednat lokálně Chemický průmysl ČR během 11 let provozu svých výroben, navrhovatelé i zákonodárci v tlaku, který vyvíjí snaha o energetických a vodohospodářských provozů, logistických legislativní smršť, překročí rámec předlouhým jednáním pečlivě komplexů a navazující infrastruktury projevil v prostředí tržní vyvážených směrnic ES a v důsledku naivity, a snad ne záměrně, ekonomiky mimořádnou odolnost vůči nepříznivým vlivům – nastaví průmyslu laťku, kterou má Evropská komise v úmyslu ztrátě východních trhů a orientaci na daleko náročnější trh uzákonit až ve svém středně nebo dlouhodobém záměru. Tak převážně zemí EU, odloučení od partnerských slovenských vznikal chemický zákon č. 157/1999 Sb., nahrazující uvádění podniků a jejich technického zázemí, rozpadu velkých výrobních látek a přípravků na trh pojmem nakládání s nimi, s nadbytečným uskupení a ztrátě obchodní infrastruktury bývalých PZO. povolováním, ohlašováním, evidencí a autorizacemi, v zemích Zahraniční kapitál se zajímal o podniky chemického průmyslu EU neznámými instituty. Rovněž ustanovením o povinném spíše výjimečně (např. Linde Technoplyn, Pliva–Lachema, pojištění vůči škodám třetím osobám a o požadavcích na rozsáhlé Silon, CHZ Sokolov, MCHZ a DEZA částečně, Česká rafi- písemné dokumenty o protihavarijní připravenosti ze zákona č. nérská, Barum Continental). Podniky dostály svým závazkům 353/1999 Sb., o prevenci závažných havárií jsme asi o roky vůči státu i zaměstnancům na rozdíl od jiných podniků tradičních předstihli právní stav, který platí v regionu, kam směřujeme – průmyslových odvětví. Dokázaly se vyrovnat s důsledky I. debaty o tzv. environmental liability tam trvají více než 10 let a generace nových právních předpisů na ochranu životního nekončí. Na rozdíl od českých právních předpisů v zemích EU prostředí - bohužel především investicemi do koncových nelze klást překážky volnému pohybu zboží, např. -
The Chemistry Development Kit (CDK). 3
Willighagen et al. RESEARCH The Chemistry Development Kit (CDK). 3. Atom typing, Rendering, Molecular Formula, and Substructure Searching Egon L Willighagen1*, John W May2, Jonathan Alvarsson3, Arvid Berg3, Nina Jeliazkova4, Tom´aˇsPluskal7, Miguel Rojas-Cherto??, Ola Spjuth3, Gilleain Torrance??, Rajarshi Guha5 and Christoph Steinbeck6 *Correspondence: [email protected] Abstract 1 Dept of Bioinformatics - BiGCaT, NUTRIM, Maastricht Background: Cheminformatics is a well-established field with many applications University, NL-6200 MD, in chemistry, biology, drug discovery, and others. The Chemistry Development Kit Maastricht, The Netherlands Full list of author information is (CDK) has become a widely used Open Source cheminformatics toolkit, available at the end of the article providing various models to represent chemical structures, of which the chemical graph is essential. However, in the first five years of the project increased so much in size that interdependencies between components grew unmanageable large, resulting in unpredictable instabilities. Results: We here report improvements to the CDK since the 1.2 release series made to accommodate both the increased complexity of the library, as well as significant improvements of and additions to the functionality of the library. Second, we outline how the CDK evolved with respect to quality control and the approach we have adopted to ensure stability, including a peer review mechanism. Additionally, a selection of the new APIs that have been introduced will be discussed: atom type perception, substructure searching, molecular fingerprints, rendering of molecules, and handling of molecular formulas. Conclusions: With this paper we have shown the continued effort to provide a free, Open Source cheminformatics library, and show that such collaborative projects can exist over a long period. -
Open Source Molecular Modeling
Accepted Manuscript Title: Open Source Molecular Modeling Author: Somayeh Pirhadi Jocelyn Sunseri David Ryan Koes PII: S1093-3263(16)30118-8 DOI: http://dx.doi.org/doi:10.1016/j.jmgm.2016.07.008 Reference: JMG 6730 To appear in: Journal of Molecular Graphics and Modelling Received date: 4-5-2016 Accepted date: 25-7-2016 Please cite this article as: Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes, Open Source Molecular Modeling, <![CDATA[Journal of Molecular Graphics and Modelling]]> (2016), http://dx.doi.org/10.1016/j.jmgm.2016.07.008 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Open Source Molecular Modeling Somayeh Pirhadia, Jocelyn Sunseria, David Ryan Koesa,∗ aDepartment of Computational and Systems Biology, University of Pittsburgh Abstract The success of molecular modeling and computational chemistry efforts are, by definition, de- pendent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. 1. Introduction What is Open Source? Free and open source software (FOSS) is software that is both considered \free software," as defined by the Free Software Foundation (http://fsf.org) and \open source," as defined by the Open Source Initiative (http://opensource.org).