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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="description" content="BioFolD - Resources">
<meta name="author" content="BioFolD - Emidio Capriotti">
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<title>BioFolD - Resources</title>
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<body>
<br>
<div class="container">
<div class="jumbotron">
<table width="100%">
<tr>
<td width="90%">
<div class='biofold' ><span style="color:#c31e27;">Bio</span><span style="color:#4689a3;">molecules</span> <span style="color:#c31e27;">Fol</span><span style="color:#4689a3;">ding and </span><span style="color:#c31e27;">D</span><span style="color:#4689a3;">isease</span></div><br>
</td>
<td width="10%">
<div class="right_cell">
<a href="http://biofold.org">
<img src="pages/img/logo.png" width="75px" align="left">
</a>
</div>
</td>
</tr>
</table>
<table width="100%">
<tr>
<td>
<div class="form-inline justify-content-center">
<nav>
<ul class="nav nav-pills">
<li role="presentation" ><a href="index.html">Home</a></li>
<li role="presentation"><a href="research.html">Research</a></li>
<li role="presentation" ><a href="people.html">People</a></li>
<li role="presentation" class='active'><a href="resources.html">Resources</a></li>
<li role="presentation"><a href="papers.html">Publications</a></li>
<li role="presentation"><a href="training.html">Training</a></li>
</ul>
</nav>
</div>
</td>
</tr>
</table>
<br>
<br>
<div class="text">
<h4 class="title" >Resources</h4>
</div>
<p class="text">
The researchers of the BioFolD Unit have developed
several web server applications that are currently hosted
on servers of the <a target=blank href="http://www.biocomp.unibo.it">University of Bologna</a>
(Italy) and maintained by other collaborators. In the future
a mirror of these applications will be made available on this server.
Currently you can reach these web servers using the following links.<br><br>
<div class="text">
<h4 class="section" >
Folding and Stability
</h4>
<table cellpadding="7" cellspacing="7" class="paper">
<tbody>
<tr><td valign="top" width=130>
<a target=blank
href="http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant/I-Mutant.cgi">
<b><p class="text">I-Mutant1.0</b></a></td>
<td valign="top"><p class="text">Neural Network based method to predict the sign of free energy change
of proteins upon single point mutation.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/15262782">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/ISMB04.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://folding.biofold.org/i-mutant/i-mutant2.0.html">
<p class="text"><b>I-Mutant2.0</b></a></td>
<td valign="top"><p class="text">Support Vector Machine based method to predict the sign and the value
of free energy change of proteins upon single point mutation.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/15980478">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/nar05.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://folding.biofold.org/k-fold">
<p class="text"><b>K-Fold</b></a></td>
<td valign="top"><p class="text">Support Vector Machine based method to predict the mechanism and
rate of protein folding kinetic.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/17138584">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/KFold_Bioinfo07.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://folding.biofold.org/k-pro">
<p class="text"><b>K-Pro</b></a></td>
<td valign="top"><p class="text">Database of kinetics data on proteins and mutants.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/turina_jmb2023.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="https://folding.biofold.org/thermoscan">
<b>ThermoScan</b></a></td>
<td valign="top"> A semi-automatic method for retrieving protein thermodynamic data from literature.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/">
<img src="../pages/img/pubmed.gif"></a>
<a href="../pages/documents/papers/">
<img width="14" src="../pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="https://folding.biofold.org/ddgun">
<b><p class="text">DDGun</b></a></td>
<td valign="top"><p class="text">Untrained method for predicting the variation of free energy change of protein mutants.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
</tbody></table>
<br>
<div class="text">
<h4 class="section" >
Genomic Variations and Disease
</h4>
<table cellpadding="7" cellspacing="7" class="paper">
<tbody>
<tr><td valign="top" width=130>
<a target=blank href="http://snps.biofold.org/contrastrank">
<p class="text"><b>ContrastRank</b></a></td>
<td valign="top">
<p class="text">Statistical method for the classification of cancer samples using exome sequencing data.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/25161249">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/Tian_Bioinformatics2014.pdf"><img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://snps.biofold.org/drcancer">
<p class="text"><b>DrCancer</b></a></td>
<td valign="top"><p class="text">Support Vector Machine based method to predict cancer-causing
mutations (Beta version).
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/21992054">
<img src="pages/img/pubmed.gif"></a>
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371640/pdf/nihms-373485.pdf"><img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank href="http://snps.biofold.org/fido-snp">
<b>Fido-SNP</b></a></td>
<td valign="top">Machine learning method for predicting the impact of SNVs in the dog genome.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/">
<img src="../pages/img/pubmed.gif"></a>
<a href="../pages/documents/papers/gkz420.pdf">
<img width="14" src="../pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://snps.biofold.org/meta-snp">
<p class="text"><b>Meta-SNP</b></a></td>
<td valign="top"><p class="text">Meta-predictor of disease causing varints that uses the output of
PANTHER, PhD-SNP, SIFT and SNAP<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/23819846">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/Capriotti_MetaSNP_BMCGenomics13.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://snps.biofold.org/phd-snp/phd-snp.html">
<p class="text"><b>PhD-SNP</b></a></td>
<td valign="top"><p class="text">Support Vector Machine based method to discriminate between neutral
or disease-related single point protein mutations.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/16895930">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/BioinfDis06.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="http://snps.biofold.org/phd-snpg">
<p class="text"><b>PhD-SNP<sup>g</sup></b></a></td>
<td valign="top"><p class="text">Machine learning method for predicting pathogenic variants in
coding and non-coding regions.
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/">
<img src="pages/img/pubmed.gif"></a>
<a href="">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
<tr><td valign="top" width=130>
<a target=blank
href="https://snps.biofold.org/snps-and-go/">
<p class="text"><b>WS-SNPs&GO</b></a></td>
<td valign="top"><p class="text">Support Vector Machine method for the detection of disease-related
SNPs based on functional information
<br>
<a target=blank href="http://www.ncbi.nlm.nih.gov/pubmed/23819482">
<img src="pages/img/pubmed.gif"></a>
<a href="pages/documents/papers/Capriotti_SNPsGO_BMCBioinformatics2013.pdf">
<img width="15" src="pages/img/pdf.gif"></a>
</td></tr>
</tbody></table>
<br>
<div class="text">
<h4 class="section" >
Macromolecular Structure
</h4>
<table cellpadding="7" cellspacing="7" class="paper">
<tbody>
<tr>
<td valign="top" width=130><a target="blank"
href="http://structure.biofold.org/sara/"><p class="text"><b>SARA</b></a></td>
<td valign="top"><p class="text">Method for RNA structure alignment and RNA functional assignment. <br />
<a target="blank" href="http://www.ncbi.nlm.nih.gov/pubmed/19483098"> <img src="pages/img/pubmed.gif" /></a> <a href="pages/documents/papers/CapriottiNAR09.pdf"> <img width="15" src="pages/img/pdf.gif" /></a></td>
</tr>
<tr>
<td valign="top" width=130><a target="blank"
href="http://www.tcoffee.org/Projects/saracoffee/"><b><p class="text">SARA-Coffee</b></a></td>
<td valign="top"><p class="text">Method for RNA multiple structure alignment <br />
<a target="blank" href="http://www.ncbi.nlm.nih.gov/pubmed/23449094"><img src="pages/img/pubmed.gif" /></a> <a href="pages/documents/papers/Kemena_Bioinformatics2013.pdf"><img width="15" src="pages/img/pdf.gif" /></a></td>
</tr>
<tr>
<td valign="top" width=130><a target="blank"
href="http://melolab.org/webrasp"><p class="text"><b>WebRASP</b></a></td>
<td valign="top"><p class="text">Method for the assessment RNA 3D structures <br />
<a target="blank" href="http://www.ncbi.nlm.nih.gov/pubmed/23929030"><img src="pages/img/pubmed.gif" /></a> <a href="pages/documents/papers/Norambuena_Bioinformatics2013.pdf"><img width="15" src="pages/img/pdf.gif" /></a></td>
</tr>
</tbody></table>
</p>
<br>
<br>
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