Poonam Mahapatra
Bioinformatics Researcher
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HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 1677 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...Gene Finding and Predictions
By Poonam Mahapatra 3056 days agogenome.crg.es - In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by...Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
By Jit 2556 days agowww.sanger.ac.uk - Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif...
Master Thesis: Trans-membrane topology prediction through Markov based decoders
By Rahul Agarwal 4191 days agoAbstract: 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...eQuant : energy-based quality assessment of protein
By Shruti Paniwala 2753 days agobiosciences.hs-mittweida.de - 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...KOBAS: a web server for gene/protein functional annotation and functional gene set enrichment
By Jit 2272 days agokobas.cbi.pku.edu.cn - KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 1481 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...SOWDHAMINI Lab
Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us...Paolo Ruggerone Lab
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...“On” and “Off” the neuron !!!
By Rahul Nayak 3909 days agoA new optogenetic protein gives neuroscientists more control over brain circuits.
