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Of possible cheminformatics futures

Tudor I. Oprea, Olivier Taboureau, Cristian G. Bologa
2011 Journal of Computer-Aided Molecular Design  
Here we address the future of cheminformatics with primary focus on innovation.  ...  Possible futures for cheminformatics include the worst case scenario (lack of funding, no creative usage), as well as the best case scenario (complete integration, from systems biology to virtual physiology  ...  Thus, the possible futures of cheminformatics are many, and their evolution is likely to help us avoid local epistemological information minima.  ... 
doi:10.1007/s10822-011-9535-9 pmid:22207193 fatcat:l2imkb3teffjhaprppkjgeeyhi

Grand challenges for cheminformatics

David J Wild
2009 Journal of Cheminformatics  
Those of us who care about the future of this field need to honestly ask whether cheminformatics is a bona-fide discipline in its own right, or whether it is a loose collection of practitioners without  ...  Editorial Welcome to the Journal of Cheminformatics.  ... 
doi:10.1186/1758-2946-1-1 pmid:20142984 pmcid:PMC2816862 fatcat:6rmdrsn7xzch5bnvqsb76uzh4u

Cheminformatics and computational chemistry in lead optimisation

Andrew R Leach
2011 Journal of Cheminformatics  
Here we will summarise some of our work to derive medicinal chemistry "rules of thumb" and to probe for possible isosteric replacements.  ...  Techniques from computational chemistry and cheminformatics have a key role to play in many aspects of lead optimisation.  ...  Here we will summarise some of our work to derive medicinal chemistry "rules of thumb" and to probe for possible isosteric replacements.  ... 
doi:10.1186/1758-2946-3-s1-o5 pmcid:PMC3083558 fatcat:dbsflbore5f3tb255ld6ydgndq

Helping to improve the practice of cheminformatics

Rajarshi Guha, Egon Willighagen
2017 Journal of Cheminformatics  
Cheminformatics practice Given the broad definition, it is useful to focus on a few areas that we feel are relevant to the future of the field.  ...  Taking a broad view, we believe that the future of cheminformatics lies in addressing large scale chemical information, across different domains.  ...  Cheminformatics practice Given the broad definition, it is useful to focus on a few areas that we feel are relevant to the future of the field.  ... 
doi:10.1186/s13321-017-0217-z pmid:29086066 pmcid:PMC5471283 fatcat:itgfagocwvferogu26bqidn634

Diversifying cheminformatics

Barbara Zdrazil, Rajarshi Guha
2022 Journal of Cheminformatics  
Barbara Zdrazil starting in her role as Co-Editor-in-Chief in January 2022, we revisit the scope of J. Cheminform, as well as the role of cheminformatics as a discipline.  ...  We present our vision for the Journal in moving the field of cheminformatics as well as Open Science forward in the coming years.  ...  Diversifying cheminformatics will only be possible with continued contributions by our community, in terms of submitting articles as well as active engagement in discussing the future role of cheminformatics  ... 
doi:10.1186/s13321-022-00597-5 pmid:35468863 pmcid:PMC9040339 fatcat:6znani6jvzd6hlxvucyrtn3lhm

Cheminformatics: Data and Standards

2022 Chemistry International  
See also Bookworm Cheminformatics: Data and Standards  ...  A call for papers was published in May 2021, with the aim of discussing cheminformatics standards and future needs.  ...  How is it possible to run meetings without meeting in-person?  ... 
doi:10.1515/ci-2022-0324 fatcat:j5ck6dh4dndotnw5n3wikca3qq

Molecular structure input on the web

Peter Ertl
2010 Journal of Cheminformatics  
And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.  ...  A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system.  ...  The future of cheminformatics, and particularly of cheminformatics applications on the web, is indeed exciting.  ... 
doi:10.1186/1758-2946-2-1 pmid:20298528 pmcid:PMC2827360 fatcat:u5yj5zdddbdfphbr36b3zeynvi

ChEMBL Beaker: A Lightweight Web Framework Providing Robust and Extensible Cheminformatics Services

Michał Nowotka, Mark Davies, George Papadatos, John Overington
2014 Challenges  
ChEMBL Beaker is an open source web framework, exposing a versatile chemistry-focused API (Application Programming Interface) to support the development of new cheminformatics applications.  ...  This paper describes the current functionality offered by Beaker and outlines the future technology roadmap.  ...  Acknowledgments We acknowledge the following people, projects and communities, without whom Beaker would not have been possible:  ... 
doi:10.3390/challe5020444 fatcat:xydn37uouzfojnerprfoyanv4a

Special Issue: Cheminformatics in Drug Discovery

Andreas Bender, Nathan Brown
2018 ChemMedChem  
importance in the future, which encouraged us to edit this Special Issue of ChemMedChem.  ...  The field of Cheminformatics was given this name in 1996 by Frank Brown, but the field and its concepts have al ong and illustrious history going back many decades, and its influence can often be seen  ...  Chemical Space Analysis The analysis of chemistry space is one of the fundamental concepts in Cheminformatics.  ... 
doi:10.1002/cmdc.201800123 pmid:29575670 fatcat:zs4wtya4yzbalnv3subis3a5oe

Extracting Relevant Information from FDA Drug Files to Create a Structurally Diverse Drug Database Using KnowItAll®

Malcolm J D'Souza, Fumie Koyoshi
2009 Pharmaceutical reviews  
These files profile approved drugs by chemical structure, solubility, absorption, distribution, metabolism, elimination, toxicity (ADME/Tox), and possible adverse reactions.  ...  It holds a large collection of in silico ADME/Tox predictors and is a chemical informatics platform used to record experimental data.  ...  This IDeA Network of Biomedical  ... 
pmid:25356090 pmcid:PMC4209477 fatcat:e5mrjokmp5derl2md5z4xw5yum

Chemical Informatics Functionality inR

Rajarshi Guha
2007 Journal of Statistical Software  
As a result, it is possible to read in a variety of molecular formats, calculate molecular descriptors and evaluate fingerprints.  ...  We describe the rcdk package that provides the R user with access to the CDK, a Java framework for cheminformatics.  ...  Hence, the integration of cheminformatics toolkits in R does not lead to a full-fledged cheminformatics modeling application.  ... 
doi:10.18637/jss.v018.i05 fatcat:2myhrdspmjaqhcoxvka43r2chm

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

Noel M O'Boyle, Chris Morley, Geoffrey R Hutchison
2008 Chemistry Central Journal  
However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++.  ...  Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files.  ...  It also aims to be as 'Pythonic' as possible; that is, to adhere to Python language conventions and idioms, and where possible to make use of Python language features such as iterators.  ... 
doi:10.1186/1752-153x-2-5 pmid:18328109 pmcid:PMC2270842 fatcat:gratmcbqabctbceq5b2rupv24y

Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment

Florian D Roessler, Oliver Korb, Andreas Bender, Werner Maentele, Peter J Bond
2012 Journal of Cheminformatics  
In addition to predictive power, MD simulations of multiple RT mutants are providing fundamental insight into the dynamics of the allosteric NNRTI binding site which is useful for the design of future  ...  predictive success of such models.  ... 
doi:10.1186/1758-2946-4-s1-p32 fatcat:zfg5qb54bzfuvbghctm7zbw4wu

Structural designing of suppressors for autisms spectrum diseases using molecular dynamics sketch

Bipin BJ Nair, Vijesh Bhaskaran, Arunjit K
2017 International Journal of Drug Delivery  
In our work we are using computational algorithm for drawing the structure of suppressor drug.  ...  <p>In this paper we are sketching the chemical structure of suppressor drug for autism spectrum disorder using a computational tool.  ...  [17] Using the Cheminformatics techniques it is possible to change the chemical structure of aautism drug with the perfect accuracy and efficiency by using the molecular dynamics concepts.  ... 
doi:10.5138/09750215.1973 fatcat:xedltrmj3je55iceve2xtpedbm

PubChem: atom environments for molecule standardization

Volker Hähnke, Evan E Bolton, Stephen H Bryant
2013 Journal of Cheminformatics  
Here, we present the first results obtained with our approach, highlighting the methodology, challenges, benefits and future possibilities. © 2013Hähnke et al.; licensee BioMed Central Ltd.  ...  Those represent 97% of the deposited structures and account for the majority of atom environments as well.  ...  Open access provides opportunities to our colleagues in other parts of the globe, by allowing anyone to view the content free of charge.  ... 
doi:10.1186/1758-2946-5-s1-p38 pmcid:PMC3606221 fatcat:nstnimdjnrberkqai4vogugyvy
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