BOL: Related items

Master Thesis: Trans-membrane topology prediction through Markov based decoders

Rahul Agarwal — Wed, 17 Jul 2013 16:16:17 -0500

Abstract:

Background/Motivation:

The dearth of structural information on alpha helical membrane protein (MPs) has hindered thus far the development of reliable knowledge –based potentials that can be used for automatic prediction of trans-membrane (TM) protein structure. While algorithm for identification of TM segments is available, modelling of the domains of alpha helical MPs involves assembling the segments into a bundle. This requires the correct assignment of the buried and lipid-exposed faces of the TM domains.

Results: In a cross validated test on single sequences, our trans-membrane MM, correctly predicts the entire topology for 77% of the sequences in a standard dataset of 86 proteins with supervised topology. These results compare favorably with existing methods.

Source Code: Matlab

Conclusion/Implementation: Here discriminant data mining approach was used to predict the location and orientation of alpha helices in membrane-spanning proteins. It is based on a first order Markov model (MM) with an architecture that corresponds closely to the biological systems. The model is enriched with three types of states for the loop on the cytoplasmic side (outer loop), loop for the non-cytoplasmic side (inner side), and trans-membrane part. The closed association between the biological and Markov states allows us to infer which part of the model architecture are important to capture the information which encodes the membrane topology, and gain a better understanding of the mechanism and constraints involved. Predictor Model was established by various Markov decoder , and assignment of the membrane helix boundaries was apparent.

eQuant : energy-based quality assessment of protein

Shruti Paniwala — Sat, 24 Jun 2017 19:24:24 -0500

Protein structures are of varying quality. Especially, in-silico modeled structures are prone to contain serious errors, which limit the usefulness and reliability of these particular protein structures.

eQuant is a service for structure quality assessment of single proteins, which utilizes a coarse-grained energy model. The overall quality is calculated as well as the reliability of individual residues. You can submit single PDB files or archives containing a set of proteins.

https://biosciences.hs-mittweida.de/equant/

Address of the bookmark: https://biosciences.hs-mittweida.de/equant/

STRUM: structure-based prediction of protein stability changes upon single-point mutation

BioStar — Mon, 10 Sep 2018 13:21:49 -0500

STRUM is a method for predicting the fold stability change (ΔΔG) of protein molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy changes on a variety of features at different levels of sequence and structure properties. The unique characteristics of STRUM is the combination of sequence profiles with low-resolution structure models from protein structure prediction, which helps enhance the robustness and accuracy of the method and make it applicable to various protein seqences, including those without experimental structures

Address of the bookmark: https://zhanglab.ccmb.med.umich.edu/STRUM/

XAMPP: Starting Apache fail Ubuntu

Ram Yash Pal — Sat, 07 Jun 2014 05:52:35 -0500

Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php

PPAI: a web server for predicting protein-aptamer interactions

Jit — Fri, 12 Jun 2020 07:26:23 -0500

PPAI can query aptamers and proteins, predict aptamers and predict protein-aptamer interactions in batch mode precisely and efficiently, which would be a novel bioinformatics tool for the research of protein-aptamer interactions. PPAI web-server is freely available at http://39.96.85.9/PPAI

Address of the bookmark: http://39.96.85.9/PPAI/

Genomic Medicine - Bruce Korf (2014)

Tue, 24 Jun 2014 07:58:44 -0500

May 21, 2014 - Current Topics in Genome Analysis 2014 A lecture series covering contemporary areas in genomics and bioinformatics. More: http://www.genome.gov/COURSE2014

RCSB PDB Sept'13 Release

Jitendra Narayan — Thu, 05 Sep 2013 15:07:48 -0500

RCSB PDB Sept'13 Release offers following new features:

- New tools to search for drugs and drug targets
- Improved interface for 3D visualisation using Jmol/JSmol
- An update to the representation of protein symmetry and stoichiometry.
- Improvements when performing sequence searches.

Reference

http://www.rcsb.org/pdb/static.do?p=general_information/whats_new.jsp?b=1308

Amino Acid Flash Tutorial

Jit — Mon, 11 Aug 2014 08:58:17 -0500

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.

How to run?

You need to install flash player or open it with web browser ( I guess you have installed flash plugin) to play.

Comment below if you like it. Thanks

Protein Subcellular Localization Prediction

Poonam Mahapatra — Thu, 01 Mar 2018 06:20:47 -0600

Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and laborious experimental methods.

http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi

Address of the bookmark: https://abi.inf.uni-tuebingen.de/Research/Systems%20Biology/protein-subcellular-localization

GrapheR !!!

John Parker — Thu, 14 Aug 2014 14:02:17 -0500

What a wonderful gem GrapheR is.... Oh yes it is. GrapheR is a GUI for base graphics in R by http://www.maximeherve.com/. The package provides a graphical user interface for creating base charts in R. It is ideal for beginners in R, as the user interface is very clear and the code is written along side into a text file, allowing users to recreate the charts directly in the console.

Adding and changing legends? Messing around with the plotting window settings? It is much easier/quicker with this GUI than reading the help file and trying to understand the various parameters.
Here is a little example using the iris data set.

library(GrapheR)
data(iris)
run.GrapheR()

This will bring up a window that helps me to create the chart and tweak the various parameters.

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!