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Chemoinformatics: Achievements and Challenges, a Personal View

Johann Gasteiger
2016 Molecules  
Computer-assisted structure elucidation and computer-assisted synthesis design have been attempted in the early years of chemoinformatics.  ...  It has become clear that chemoinformatics can have applications in any field of chemistry and related sciences.  ...  Acknowledgments: I gratefully acknowledge the contribution of an anonymous reviewer for his helpful comments and for providing additional references.  ... 
doi:10.3390/molecules21020151 pmid:26828468 fatcat:liarryjq5nearphstvytubcogq

Chemistry in Times of Artificial Intelligence

Johann Gasteiger
2020 ChemPhysChem  
, and the elucidation of the structure of molecules.  ...  Chemoinformatics has found important applications in the fields of drug discovery, analytical chemistry, organic chemistry, agrichemical research, food science, regulatory science, material science, and  ...  After ventures into experimental and theoretical chemistry I was fortunate to be able to develop the field of chemoinformatics together with inspiring colleagues.  ... 
doi:10.1002/cphc.202000518 pmid:32808729 fatcat:o2mnjpgo7vaepdbpom4otfdgae

Advancing Cheminformatics—A Theme Issue in Honor of Professor Jürgen Bajorath

Martin Vogt
2022 Molecules  
While cheminformatics problems have been actively researched since the early 1960s, as witnessed by the QSAR approaches developed by Toshio Fujita and Corwin Hansch [...]  ...  Of course, structure activity relationship (SAR) and structure property relationship (SPR) research themselves are at the heart of cheminformatics and quantitative SAR studies, i.e., the mathematical modeling  ...  Bajorath in a single phrase, it might be "method development for qualitative and quantitative structure activity/property relationships".  ... 
doi:10.3390/molecules27082542 pmid:35458738 pmcid:PMC9028174 fatcat:4dltbjc7jjeczkopt4zddokj4e

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics

Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon Willighagen
2003 Journal of chemical information and computer sciences  
, structure diagram generation, etc.  ...  The Chemistry Development Kit (CDK) is a freely available open-source Java library for Structural Chemoand Bioinformatics.  ...  ACKNOWLEDGMENT The authors would like to thank all members of the CDK project for their contributions, corrections, and helpful comments.  ... 
doi:10.1021/ci025584y pmid:12653513 pmcid:PMC4901983 fatcat:owqxli2qi5dmnl637ualxiriji

Chemometrics in Medicine and Pharmacy

Ján Mocák
2012 Nova Biotechnologica et Chimica  
This minireview summarizes the basic ways of application of chemometrics in medicine and pharmacy.  ...  The aim of this contribution is a brief presentation of versatile potentialities of contemporary chemometrical techniques and relevant software.  ...  QSPR (Quantitative Structure -Property Relationships) connects the knowledge from biology, chemistry, physics, mathematics, and computer sciences with the aim of exploring properties of substances and  ... 
doi:10.2478/v10296-012-0002-3 fatcat:vznml2pjsre3vgc32jwsuw4bhm

Molecular Optimization Using Computational Multi-Objective Methods

C.A. Nicolaou, N. Brown, C.S. Pattichis
2007 Zenodo  
Traditionally, standard chemoinformatics methods ignored this problem and focused on the sequential optimization of each single biological or chemical property (ie, a single objective).  ...  This paper first presents a brief introduction to issues related to MOOP and then surveys the application of MOOP methods in the field of chemoinformatics.  ...  recursive partitioning, QSAR quantitative structure-activity relationship, QSPR quantitative structure-property relationship. equivalent common substructures [13• ].  ... 
doi:10.5281/zenodo.2555799 fatcat:r4d75kodwjatppw2z4yohbdsva

From chemical documentation to chemoinformatics: 50 years of chemical information science

Peter Willett
2008 Journal of information science  
technology to chemical problems; and the use of statistical correlation methods for the prediction of molecular properties (called QSAR for quantitative structure-activity relationships).  ...  For example, similarity and generic searching methods were developed to complement structure and substructure searching, and the much enhanced computer technology of the time enabled the widespread implementation  ...  I thank Val Gillet and Wendy Warr for their comments on this paper.  ... 
doi:10.1177/0165551507084631 fatcat:3fdz6z6mizgthfjzsr4qty4fty

تطویر برنامج اعداد معلم الکیمیاء بکلیات التربیة فی ضوء المعلوماتیة الکیمیائیة chemoinformatics

دعاء سعید محمود إسماعیل
2019 مجلة الجمعیة المصریة للتربیة العلمیة  
and QASR (the well -known Quantitative structure - activity relationship. ‫  ...  QSAR (Quantitative Structure Activity Relationship) methods . ‫ٚ  ... 
doi:10.21608/mktm.2019.114040 fatcat:pp3jnrtkfrdnvdlmxvifimju6m

Similarity methods in chemoinformatics

Peter Willett
2009 Annual Review of Information Science and Technology  
a range of simpler, and computationally much less-demanding, approaches to the same end (Hinchcliffe, 2003; Leach, 2001) , and quantitative structure-activity relationship (QSAR) studies, which seek  ...  relationships between chemical structure and biological activity.  ... 
doi:10.1002/aris.2009.1440430108 fatcat:3spez43we5bthe7nfzy45c3kka

Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor

Chia-Hsien Lee, Hsuan-Cheng Huang, Hsueh-Fen Juan
2011 International Journal of Molecular Sciences  
In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity  ...  Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches.  ...  QSAR QSAR, which stands for "quantitative structure-activity relationships", is a method that relates chemical structure to biological or chemical activity using mathematical models [31] .  ... 
doi:10.3390/ijms12085304 pmid:21954360 pmcid:PMC3179167 fatcat:rwsusxs7lnajdig3jmxek2wfoi

Theoretical and computational approaches to ligand-based drug discovery

Angelo, D. Favia
2011 Frontiers in Bioscience  
Quantitative structure-properties relationships have been successfully used for several years in a vast number of fields.  ...  Mathematical applications are then used to find quantitative relationships between the descriptors and the measured activities.  ... 
doi:10.2741/3788 pmid:21196231 fatcat:662k45uccfdedhxds332uresl4

Quantitative Methods in System-Based Drug Discovery [chapter]

Yu-Chen Lo, Ren Gui, Hiroshi Honda, Jorge Z. Torres
2016 Complex Systems, Sustainability and Innovation  
This is followed by a discussion on structure-based drug design and statistical tools for pharmaceutical research.  ...  In this chapter, we provide an overview of quantitative methods for system-based drug discovery.  ...  Structure-based approaches to drug design Modern medicinal chemistry methods and molecular modeling have been employed as powerful tools for the study of structure-activity relationships S"R [ ].  ... 
doi:10.5772/65833 fatcat:r44luaviovb5dnda7jmr5wjxdm

Quantitative Structure–Selectivity Relationships in Enantioselective Catalysis: Past, Present, and Future

Andrew F. Zahrt, Soumitra V. Athavale, Scott E. Denmark
2019 Chemical Reviews  
This review summarizes strategies to employ quantitative structure-selectivity relationships (QSSR) in asymmetric catalytic reactions.  ...  In the past two decades, chemoinformatics, the application of informatics to solve problems in chemistry, has increasingly influenced prediction of activity and mechanistic investigations of organic reactions  ...  Specifically, his research includes using applied quantum chemistry to garner mechanistic insights in catalytic reactions and developing strategies incorporating chemoinformatics and machine learning to  ... 
doi:10.1021/acs.chemrev.9b00425 pmid:31886649 pmcid:PMC7018559 fatcat:pwz5fe5g3nhjtnl3bbxldffgsu

SMMRNA: a database of small molecule modulators of RNA

Ankita Mehta, Surabhi Sonam, Isha Gouri, Saurabh Loharch, Deepak K. Sharma, Raman Parkesh
2013 Nucleic Acids Research  
We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening.  ...  The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling.  ...  ACKNOWLEDGEMENTS The authors thank Dr Rethi Madathil for help in preparing the manuscript, Ms Isha for drawing additional structures and clustering analysis and Dr Kundan, Dr Ganesh and Mr Kiran for technical  ... 
doi:10.1093/nar/gkt976 pmid:24163098 pmcid:PMC3965028 fatcat:wfjlwufldvhelbbsllpfw2nrsu

Natural product drug discovery in the artificial intelligence era

Fernanda I Saldivar-Gonzalez, Victor Daniel Aldas-Bulos, José Luis Medina-Franco, Fabien Plisson
2022 Chemical Science  
Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even...  ...  Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets.  ...  More recently, 3D fingerprints have been reported to predict and rank the biological activities from chemical structures, the so-called Quantitative Structure-Activity/Property Relationship (QSA/PR) models  ... 
doi:10.1039/d1sc04471k pmid:35282622 pmcid:PMC8827052 fatcat:jyfupubc2bgb7p4v6b62apgtfq
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