BOL: Related items

Paolo Ruggerone Lab

Tue, 01 Oct 2013 14:15:53 -0500

Efflux pumps (RND family)

Functioning of efflux systems in Gram-negative bacteria
Determinants of the compound-efflux system interactions
Action of inhibitors on efflux systems
Structural and dynamical features of the efflux systems

TatA
Assembly of the TatA system
Study of the dynamical features of the charge zipper

Methods
Setup of a kinetic Monte Carlo (KMC) scheme to study the flux of antibiotics through porins and efflux systems
Setup of protocol to integrate MD results in a ligand-based approach

Viral inhibitors
Interactions of selected compounds with RNA-dependent RNA polymerases (RdRps) of HCV and BVDV
Assessment of the role of mutations in RdRps
Antimicrobial peptides

Interactions of antimicrobial peptides with membranes: structure and dynamics
Interactions between antimicrobial peptides in the presence of different membranes
Protein-protein interactions
Effects of mutations

Lab Page
http://www.dsf.unica.it/~paolo/Site/Home.html

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

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

MetaPred2CS

Manisha Mishra — Fri, 03 Mar 2017 05:15:07 -0600

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component system protein-protein interactions (PPIs). The methods implemented in MetaPred2CS are 2 co-evolutionary methods: in-silico two hybrid (i2h) and mirror tree (MT) methods and 4 genomics context based methods: phylogenetic profiling (PP), gene fusion (GF), gene neighbourhood (GN) and and gene operon methods (GO).

http://metapred2cs.ibers.aber.ac.uk/

Address of the bookmark: https://github.com/martinjvickers/MetaPred2CS

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

Tools for Protein-Protein Docking !

Poonam Mahapatra — Wed, 25 Apr 2018 05:15:53 -0500

Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Following are the tools to predict the structure of protein–protein complexes:

3D-Dock Suite

Global rigid search: FFTShape complementarity and electrostatics

Re-scoring and clustering. Refinement of interface side-chains

3D-Garden

Global rigid search in ensamble

Shape complementarity and Lennard–Jones potential

Side chain and backbone dihedral refinement

DOT

Global rigid search: FFTShape complementarity, electrostatics and VDWNone

Escher NG

Global rigid searchShape complementarity, hydrogen bonds and electrostatic

Integrated in VEGA

GRAMM

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potential

Clustering of conformations

GRAMM-X

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters

HEX

Global rigid search: Fourier correlation of spherical harmonics

Shape complementarity

HADDOCK

Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data.

ICM

Global rigid search: Monte CarloEmpirical scoring function

Clustering and selection of conformations. Refinement of interface side-chains and re-scoring

MolFit

Global rigid search: FFTShape complementarity

Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations

PatchDock

Global rigid searchShape complementarity and atomic desolvation energy

Clustering of conformations

PyDock

Global rigid search:FFTShape complementarity

rescoring by binding electrostatics and desolvation energy

RosettaDock

Local rigid search: Monte Carlo with low and high resolution structure representation levels

Different scoring parameters for the different resolutions

ZDOCK

Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.

Energy minimization and re-scoringFree for academics

Point to note:

The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

How DNA is Packaged (Advanced)

Mon, 23 Sep 2013 18:08:34 -0500

Each chromosome consists of one continuous thread-like molecule of DNA coiled tightly around proteins, and contains a portion of the 6,400,000,000 basepairs (DNA building blocks) that make up your DNA. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is formed when eight separate histone protein subunits attach to the DNA molecule. The combined tight loop of DNA and protein is the nucleosome. Six nucleosomes are coiled together and these then stack on top of each other. The end result is a fiber of packed nucleosomes known as chromatin. This structure, is then looped and further packaged using other proteins (which are not shown here) to give the final "chromosomal" shapes. It is this remarkable multiple folding which allows six feet of DNA to fit into the nucleus of each cell in our body. And a typical cell nucleus is so small that ten thousand could fit on the tip of a needle. It is important to realize that chromosomes are not always present, they form only when cells are dividing. At other times, as we can see here at the end of cell division, our DNA becomes less highly organized.)

Edit DNA !!!

Jit — Wed, 05 Mar 2014 02:27:54 -0600

A genome-engineering tool known as Crispr may allow scientists to alter the DNA of humans, animals and plants, a research breakthrough that promises to make a significant impact on science and fighting diseases, according to a March 3 story in the New York Times. Scientists hope Crispr might also be used for genomic surgery, as it were, to correct errant genes that cause disease.

A rescently publication paper ( http://jb.asm.org/content/169/12/5429.long )shows significance of an unusual repeated DNA sequences next to a gene in a common bacterium, and their scientific significance. The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life. This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows “customizing the genome of any cell or any species at will,”.

Reference:

http://www.prweb.com/releases/2014/03/prweb11636031.htm

http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html?hpw&rref=health

http://jb.asm.org/content/169/12/5429.long

Scripted DNA !!!

Jit — Mon, 17 Aug 2015 17:44:04 -0500

As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)