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AlphaFold for Protein Structure Prediction: Unlocking Nature’s 3D Secrets

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In the fascinating world of bioinformatics, understanding the intricate structures of proteins is like deciphering the blueprints of life. Proteins play critical roles in our bodies, from catalyzing chemical reactions to maintaining cellular structures. But how do we unveil their hidden shapes? Enter AlphaFold , an AI marvel that has revolutionized protein structure prediction. Decoding the Mystery: Protein Structure Prediction Proteins are made up of amino acids, strung together like beads on a necklace. Their sequence is encoded in our genes, but their 3D structures remain elusive. Why does structure matter? Because it determines protein function! Imagine a lock (protein) and its key (molecule). If the key doesn’t fit precisely, the lock won’t open – and that’s where AlphaFold steps in. The Problem: From Sequence to Structure Challenge : Given a protein’s amino acid sequence, predicting its 3D structure is akin to solving a complex puzzle. Historical Struggles : Scientists have...
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MA/M.Sc. Mathematics Dissertation Topics

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Considering the syllabus of the Private Examination Cell (PEC) at Sambalpur University , here are some dissertation topics for your MA / M.Sc Mathematics studies. You can explore these topics while also applying programming languages such as Python , C , or C++ : Numerical Methods and Computational Mathematics : Investigate numerical techniques for solving differential equations, linear algebra problems, or optimization problems. Implement algorithms in Python or C++ to approximate solutions efficiently. Graph Theory and Network Analysis : Explore graph algorithms, connectivity, coloring, or centrality measures. Write code to analyze real-world networks using Python or C++. Mathematical Modeling in Ecology or Epidemiology : Develop mathematical models for population dynamics, disease spread, or ecological systems. Use Python to simulate and analyze the behavior of these models. Statistical Inference and Data Analysis : Study statistical methods, hypothesis testing, regression, or Bay...
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Pandoc: Document format converter

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Pandoc - Document Converter Came across this tool on Ubuntu - Pandoc - Universal Document Converter. Very handy tool to convert between different formats. I had to convert a LibreOffice Writer document to EPUB format. pandoc test.odt -f odt -t epub -s -o test.epub test.odt - original document in odt format -f - input format -t - output format -s - standalone document -o - output file
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NCBI Standalone BLAST

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Using the standalone NCBI BLAST I am describing the use of a standalone BLAST () on a Ubuntu 22.04.4 LTS system. You can get a lot of details at the NCBI BLAST Manual site . I will stick to the components i require for my work. Building a BLAST database from local sequences The makeblastdb application produces BLAST databases from FASTA files.  Use the –parse_seqids flag when invoking makeblastdb to enable retrieval of sequences based upon sequence identifiers. It is  possible to fetch individual sequences using blastdbcmd or to limit the search with the –seqidlist option.  In this case, each sequence must have a unique identifier, and that identifier must have a specific format. The identifier should begin right after the “>” sign on the definition line, contain no spaces. specify its type ( -dbtype nucl/prot) name the output database with the same base name ( -out hs_chr) overwriting the existing one. -title for name of the Database makeblastdb -in ...
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