Search Results for "amino"
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Showing 66 open source projects for "amino"
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Deploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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Repfabric is a customer relationship management (CRM) software designed specifically for multi-line sales teams (i.e. reps, distributors, wholesalers, dealers, and manufacturers). It streamlines and simplifies the sales process by providing deep integration with email, contacts, calendars, and deal tracking. The platform enables users to track commissions from CRM to sale, make updates directly from mobile devices, and document sales calls using voice-to-text features.
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Alphafold2
Unofficial Pytorch implementation / replication of Alphafold2
To eventually become an unofficial working Pytorch implementation of Alphafold2, the breathtaking attention network that solved CASP14. Will be gradually implemented as more details of the architecture is released. Once this is replicated, I intend to fold all available amino acid sequences out there in-silico and release it as an academic torrent, to further science. Deepmind has open sourced the official code in Jax, along with the weights! This repository will now be geared towards... -
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AstroBioTools
Adaptive analysis of amino acid alphabets
A new, fast implementation of algorithms used for the adaptive analysis of amino acid alphabets as described in Philip, G. K., & Freeland, S. J. (2011). Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology, 11(3), 235-240. Ilardo, M., Meringer, M., Freeland, S., Rasulev, B., & Cleaves II, H. J. (2015). Extraordinarily adaptive properties of the genetically encoded amino acids. Scientific reports, 5, 9414. Ilardo, M., Bose, R., Meringer, M., Rasulev, B... -
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Mutation2 Rust
Program to show point mutation, insertion and deletion on DNA, RNA
You can watch the result of point mutation, insertion and deletion on a short strand of DNA, the complementary strand of RNA and the Amino Acids -
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AmPEP and AxPEP
Sequence-based Antimicrobial Peptide Prediction by Random Forest
Antimicrobial peptides (AMPs) are promising candidates in the fight against multidrug-resistant pathogens due to its broad range of activities and low toxicity. However, identification of AMPs through wet-lab experiment is still expensive and time consuming. AmPEP is an accurate computational method for AMP prediction using the random forest algorithm. The prediction model is based on the distribution patterns of amino acid properties along the sequence. Our optimal model, AmPEP with 1:3 data... -
Track all your service data in one easy-to-use system, enabling your team to move faster and generate more revenue for your bottom line.
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ResidueFinder is available for use, modified from MutationFinder. Residue finder, mutation, amino acid.
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Teresa
Nutrition program
Control the wanted quantities of macro-nutrients, vitamins, minerals and amino acids allowing this program to choose for you proper doses of food with the best price -
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qmol
A simple molecular weight calculator
qmol is a simple molecular weight calculator, available for Linux and Windows, derived from Tomislav Gountchev's KMol. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %). See the features list below for more details or consult the wiki page: https://sourceforge.net/p/qmol/wiki/Home/. For Windows binary and source code see the files section:... -
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MetaPA is a de Bruijn graph algorithm to obtain complete protein coding genes by assembling metagenomic and metatranscriptomic short reads. Jiemeng Liu*, Qichao Lian*, Yamao Chen, Ji Qi. (2019) Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads. Nucleic Acids Research.
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
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Deliver a personalized customer experience with every interaction, across every channel, with uContact, net2phone’s cloud contact center solution.
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
Understanding protein interaction with material surfaces is important for the development of nanotechnological devices. The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set... -
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
... the second order tensor of the Hessian from molecular fragments. The output has been made compatible with the Gromacs topology format. Examples of use include the derivation of bond force constants and equilibrium values for: -bonded metals in protein active sites -modified amino acids -small molecules/drug molecules A zip of examples files can be found by following the "Browse All Files" link. Written by Dr Anthony Nash (Oxford) Supported by Dr Thomas Collier, Prof Helen Birch & -
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CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
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Nutrition Tables
Nutrition Investigator
This Nutrition Software consists of easy modifiable tables of selected food nutrients in one file, helps to make an individual diet. The information in this file was obtained from: Source (or Adapted from, as appropriate): Canadian Nutrient File, Health Canada, 2010 and other sources. This file gives an idea of which nutrient could be more likely found in fair quantities in some product. Use that file as a reference tool. Do not make any diet plans based on this information only,... -
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Fragment-based Peptide Docking
Fragment-based Peptide Docking
A fortran based fragmentizing-docking-remerging program for long peptides (10-16 amino acids) docking simulations. This program is compiled by intel fortran at OpenSUSE 64-bits. Designed for 4GPU servers. NOTE: AMBER software packages, AMBER Tools and pmemd.cuda must be normally installed to fully operate this program. However you can still sample massive initial structures (500k~2m peptide conformations) without AMBER. Reference: http://pubs.rsc.org/en/content/articlelanding/2017/cp... -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
... solutions. MSTgold accepts single-character data that are nucleotides, amino acids, binary characters, or SNPs; integers that represent, for instance, the lengths of VNTRs or microsatellites; and distance matrices. The MSTgold package includes Mac OS X, Linux, and Windows executables of the MSTgold program, a detailed Manual, example data and results, and executables of the program Fasta2MSTG which converts Fasta sequence files to the MSTgold input format. -
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PPA D
A method for predicting the locations of protein antigenic determinant
A computerized method for predicting the locations of protein antigenic determinants is presented, which requires only the amino acid sequence of a protein, and no other information. This procedure has been used to predict the major antigenic determinant of the hepatitis B surface antigen, as well as antigenic sites on a series of test proteins of known antigenic structure. The method is suitable for use in smaller personal computer, and is written in C++ in order to make it available... -
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RAPSearch2
Reduced Alphabet based Protein similarity Search
RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing. -
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DaMold
a data mining platform for variant annotation and visualization.
DaMold a powerful, integrated, web-based, and user-friendly tool to filter, annotate, cross-link, and visualize NGS, Sanger, and hotspot variants. It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs... -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
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PROMOT
A tool for finding functional motifs from aligned protein sequences
... The above command sets fitness threshold to 70%, number of choices per motif element to 2, and ignores the functional grouping of the amino-acids, asking to input the data from aligned.fasta and redirecting the tool output to output.txt. You can open output.txt to view the results of the execution. -
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HotDriver is a python program that is designed to employ the Poisson statistical model to predict hotspot mutations in single amino acid level given a mutation dataset. Please refer to the README.txt to understand how to properly use HotDriver in your own study. Please contact tchen1@mdanderson.org or kchen3@mdanderson.org if you may have any questions.
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Software for visualization of point variability in pairwise sequence alignment FASTA format. Featuring GUI interface, this simple application enables insight into variation of nucleic and amino acids on specific loci. Current 1.1 version supports amino and nucleic acid alignments. There are 2 variations of this software. One is CLI based and the other one is GUI based. Read corresponding README files in order to get familiar with the software. Extract files and run the jar file!
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work in progress. ResidueFinder section is available for use, modified from MutationFinder. Residue finder, mutation, amino acid.
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Sequencia
Protein Primary Sequnece Analysis
The current work is focused on the Software Development of an Offline Tool for “PRIMARY-SEQUENCE ANALYSIS” with JAVA and open source resources. SEQUENCIA Tool is an offline Tool of Primary Sequence Analysis, which is quite prevalent Topic for Researchers all over the world. Sequence Name, Sequence Length, Absorbance, Net charge, Iso electric charge, Amino acid composition, Amino acid classification, Aliphatic Index, Instability Index, Average Hydropathy etc are the Primary Sequence Analysis... -
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nagnag
Identifyng and Quantifying NAGNAG Alternative Splicing
The NAGNAG alternative splicing is a regulatory process that controls the mRNA splicing from one gene. NAGNAG alternative splicing has attracted intensive attentions for last decades because of its unique property: inclusion or exclusion of three nucleotides results in difference of one or two amino acids in the final proteins.