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Related Concept Videos

Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

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Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
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Metal-Ligand Bonds02:51

Metal-Ligand Bonds

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The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Group Design02:01

Group Design

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The most basic experimental design involves two groups: the experimental group and the control group. The two groups are designed to be the same except for one difference— experimental manipulation. The experimental group gets the experimental manipulation—that is, the treatment or variable being tested—and the control group does not. Since experimental manipulation is the only difference between the experimental and control groups, we can be sure that any differences between...
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Structural Isomerism02:34

Structural Isomerism

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Isomerism in Complexes
Isomers are different chemical species that have the same chemical formula. Structural isomerism of coordination compounds can be divided into two subcategories, the linkage isomers and coordination-sphere isomers.
Linkage isomers occur when the coordination compound contains a ligand that can bind to the transition metal center through two different atoms. For example, the CN− ligand can bind through the carbon atom or through the nitrogen atom. Similarly, SCN− can...
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Ligand- and Structure-Based Drug Design and Optimization using KNIME.

Michael P Mazanetz1,2, Charlotte H F Goode2, Ewa I Chudyk3

  • 1NovaData Solutions Ltd., PO Box 639, Abingdon-on-Thames, Oxfordshire OX14 9JD, United Kingdom

Current Medicinal Chemistry
|April 10, 2019
PubMed
Summary
This summary is machine-generated.

Data mining and accessible tools accelerate drug discovery. The KNIME platform, a leading open-source analytics tool, enhances early-stage drug design and development, improving success rates for new medicines.

Keywords:
ADME modellingHit expansionKNIMEbig datacomputer-aided drug designdata miningligand optimisationpredictive toxicologyvirtual screeningworkflows

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Area of Science:

  • Computational chemistry
  • cheminformatics
  • drug discovery informatics

Background:

  • The drug discovery process has been revolutionized by data mining and accessible tools, significantly shortening timelines and improving success rates.
  • The Konstanz Information Miner (KNIME) is an open-source data analytics platform that has been pivotal in advancing drug discovery for over ten years.
  • KNIME offers a comprehensive suite of tools and a strong community support system for both ligand- and structure-based drug design.

Purpose of the Study:

  • To review recent advancements in the KNIME platform specifically for small-molecule drug design.
  • To provide insights into the current challenges and future directions in applying KNIME to drug discovery.

Main Methods:

  • Review of recent developments and applications of the KNIME platform in drug discovery.
  • Analysis of KNIME's capabilities in supporting ligand- and structure-based small-molecule drug design.

Main Results:

  • KNIME has evolved with new tools and features to support modern drug discovery workflows.
  • The platform's open-source nature and community support facilitate its adoption and customization for various drug design tasks.

Conclusions:

  • KNIME is a powerful and versatile platform that significantly aids in accelerating early drug discovery.
  • Continued development and community contributions will further enhance KNIME's role in addressing future challenges in small-molecule drug design.