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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36395?offset=160</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</guid>
	<pubDate>Tue, 18 Jun 2024 02:04:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44581/biokit-a-set-of-tools-dedicated-to-bioinformatics-data-visualisation</link>
	<title><![CDATA[BioKit: a set of tools dedicated to bioinformatics, data visualisation]]></title>
	<description><![CDATA[<p><span>BioKit is a set of tools dedicated to bioinformatics, data visualisation (</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.viz" title="biokit.viz"><code><span>biokit.viz</span></code></a><span>), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g.,&nbsp;</span><a href="https://biokit.readthedocs.io/en/latest/references.html#module-biokit.stats" title="biokit.stats"><code><span>biokit.stats</span></code></a><span>). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).</span></p><p>Address of the bookmark: <a href="https://biokit.readthedocs.io/en/latest/index.html" rel="nofollow">https://biokit.readthedocs.io/en/latest/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42354/vsfilt-a-tool-to-improve-virtual-screening-by-structural-filtration-of-docking-poses</guid>
	<pubDate>Wed, 25 Nov 2020 02:39:16 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42354/vsfilt-a-tool-to-improve-virtual-screening-by-structural-filtration-of-docking-poses</link>
	<title><![CDATA[vsFilt: A tool to improve virtual screening by structural filtration of docking poses]]></title>
	<description><![CDATA[<p><span>The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, &pi;-stacking, and cation-&pi; interactions. The web-server can process large libraries of up to 150&rsquo;000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.</span></p><p>Address of the bookmark: <a href="https://biokinet.belozersky.msu.ru/vsfilt" rel="nofollow">https://biokinet.belozersky.msu.ru/vsfilt</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</guid>
	<pubDate>Fri, 27 Sep 2013 04:24:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</link>
	<title><![CDATA[Molecular Genetics Lecture]]></title>
	<description><![CDATA[<p><span>"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."&nbsp;</span></p>
<p><span>"<span><strong>Robert Sapolsky</strong> is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia</span></span></p><p>Address of the bookmark: <a href="http://www.youtube.com/watch?v=_dRXA1_e30o" rel="nofollow">http://www.youtube.com/watch?v=_dRXA1_e30o</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding</guid>
	<pubDate>Thu, 24 May 2018 02:53:31 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36752/minmax-a-versatile-tool-for-calculating-and-comparing-synonymous-codon-usage-and-its-impact-on-protein-folding</link>
	<title><![CDATA[%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.]]></title>
	<description><![CDATA[%MM calculates whether a given gene sequence encodes amino acids using the most common codons possible, the least common codons possible, or (most typically) some combination of these extremes. See our PLoS ONE paper for more details on how the %MinMax algorithm works. 

%MinMax results are averaged over an 18-codon sliding window; hence the result for "codon window = 1" is the average codon usage for codons 1-18, codon window 2 = codons 2-19, etc.<p>Address of the bookmark: <a href="http://www.codons.org/" rel="nofollow">http://www.codons.org/</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify</guid>
	<pubDate>Tue, 05 Mar 2024 00:23:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify</link>
	<title><![CDATA[doubletrouble: identify duplicated genes from whole-genome protein sequences and classify]]></title>
	<description><![CDATA[<p><span>doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.</span></p><p>Address of the bookmark: <a href="https://bioconductor.org/packages/release/bioc/html/doubletrouble.html" rel="nofollow">https://bioconductor.org/packages/release/bioc/html/doubletrouble.html</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5209/anders-krogh-lab</guid>
  <pubDate>Mon, 30 Sep 2013 19:07:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Anders Krogh Lab]]></title>
  <description><![CDATA[
<p>In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene identification (refs) and have worked on methods for such things as discriminative estimation of HMMs (refs) and alternative decoding algorithms etc. (refs).</p>

<p>Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages. </p>

<p>Lab page @ http://wiki.binf.ku.dk/User:Krogh</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/6562/molecular-bioinformatics-lab-mbl</guid>
  <pubDate>Tue, 19 Nov 2013 18:23:27 -0600</pubDate>
  <link></link>
  <title><![CDATA[Molecular Bioinformatics Lab (MBL)]]></title>
  <description><![CDATA[
<p>The main subject of interest in our laboratory is the study of the relationship among sequence, structure, and function in proteins and nucleic acids. Our research can be divided in two major topics:</p>

<p>the study of the sequence-structure relationship<br />(application -&gt; structure prediction)<br />the study of the structure-function relationship<br />(application -&gt; function prediction)</p>

<p>Therefore, anything related to the configuration (sequence) and conformation (structure) in atomic systems of proteins and nucleic acids, and the interaction of these with other elements (function) is of our major interest.</p>

<p>Lab page @ http://melolab.org/mbl/</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10260/%E2%80%9Con%E2%80%9D-and-%E2%80%9Coff%E2%80%9D-the-neuron</guid>
	<pubDate>Fri, 25 Apr 2014 19:31:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10260/%E2%80%9Con%E2%80%9D-and-%E2%80%9Coff%E2%80%9D-the-neuron</link>
	<title><![CDATA[“On” and “Off” the neuron !!!]]></title>
	<description><![CDATA[<p><span>Optogenetics is a recent innovation in neuroscience that gives researchers the ability to control the activity of neurons with light. With this powerful tool, researchers are teasing apart the biological basis of memory, behavior, and disease (see &ldquo;<a href="http://www.technologyreview.com/news/517226/scientists-make-mice-remember-things-that-didnt-happen/"><span>Scientists Make Mice &lsquo;Remember&rsquo; Things That Didn&rsquo;t Happen</span></a>&rdquo; and &ldquo;<a href="http://www.technologyreview.com/news/423254/an-on-off-switch-for-anxiety/"><span>An On-Off Switch for Anxiety</span></a>,&rdquo;). But for the first several years of this technology&rsquo;s existence, the proteins that scientists added to neurons to make them react to light were only good at activating neurons. That limited researchers&rsquo; ability to understand neuronal circuits, sets of interconnected neurons that are thought to control behavior and, when misfiring, to underlie many brain conditions. Problems can arise from any imbalance in circuit activity, whether too much or too little.&nbsp;</span></p><p><span>Now, two research groups have engineered new optogenetic proteins that can be used to efficiently silence neurons.&nbsp;<span><span>One of the two new proteins comes from the lab of<span>&nbsp;</span><a href="http://www.stanford.edu/group/dlab/about_pi.html" target="_blank">Karl Deisseroth</a>, a psychiatrist and neuroscientist at Stanford University who helped develop optogenetics as a research tool.&nbsp;His group&rsquo;s new &ldquo;off&rdquo; switch for neurons was created by changing 10 of the 333 amino acids in an existing optogenetic protein, which itself had been engineered by combining natural proteins from<span>&nbsp;</span></span></span><a href="http://genome.jgi-psf.org/Chlre3/Chlre3.home.html" target="_blank"><span>green algae</span></a><span><span>. That advance&nbsp;</span><span>&ldquo;creates a powerful tool that allows neuroscientists to apply a brake in any specific circuit with millisecond precision,&rdquo; said Thomas&nbsp;Insel, director of the National Institute of Mental Health, in a released statement.&nbsp;</span><a href="http://www.sciencemag.org/content/344/6182/409" target="_blank"><span>The other new silencing protein</span></a>, developed by scientists at the H</span><span>umboldt University of Berlin and collaborators, was created by changing amino acids in the same existing optogenetic protein.&nbsp;</span></span></p><p><span><span>Some researchers are also looking to optogenetics as a potential treatment for patients with a variety of conditions (see &ldquo;</span></span><span><a href="http://www.technologyreview.com/news/524771/for-mice-and-maybe-men-pain-is-gone-in-a-flash/"><span>For Mice, and Maybe Men, Pain Is Gone in a Flash</span></a><span><span>,&rdquo; and &ldquo;</span></span><a href="http://www.technologyreview.com/news/506981/flipping-on-the-lights-to-halt-seizures/"><span>Flipping on the Lights to Halt Seizures</span></a><span><span>&rdquo;) but there are huge challenges to overcome. The method requires genetic modification of cells to make them light-sensitive. It also requires implanted light sources for all but the shallowest of nerve endings. <br /></span></span></span></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/13911/amino-acid-flash-tutorial</guid>
	<pubDate>Mon, 11 Aug 2014 08:58:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/13911/amino-acid-flash-tutorial</link>
	<title><![CDATA[Amino Acid Flash Tutorial]]></title>
	<description><![CDATA[<p>Protein is a part of every cell in your body, and no other nutrient plays as many different roles in keeping you alive and healthy. Protein is the building block of our body, and amino acids are the main areas of interest. We have emphasized on all 20 amino acids in this documentary movie. This documentary has been developed that emphasize on chemical structure, chemical formula, IUPAC name and other detail information of all 20 amino acids with the voice, picture with interactive button. This will be helpful for the entire biology and bioinformatics student.</p><p>How to run?</p><p>You need to install flash player or open it with web browser ( I guess you have installed flash plugin) to play.</p><p>Comment below if you like it. Thanks</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/13911" length="33435911" type="application/x-shockwave-flash" />
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur</guid>
  <pubDate>Tue, 07 Jul 2015 23:12:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[BISR Jaipur]]></title>
  <description><![CDATA[
<p>The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:</p>

<p>    Bioinformatics supports to researchers<br />    Customized training in Bioinformatics for researchers and faculty members<br />    Support in Installing, implementing and maintaining software on computer.<br />    Create awareness for taking preventive measure against data security<br />    Organize workshops on thrust ares of Bioinformatics<br />    Research Training to students of Biotechnology and Bioinformatics </p>

<p>More at http://bioinfo.bisr.res.in/index.php</p>
]]></description>
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