Search Results for "amino java"
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Showing 17 open source projects for "amino java"
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ForceGen
Derives force constants from Gaussian QM for Gromacs MD
Please cite: ForceGen: atomic covalent bond constant derivation for Gromacs. Nash A, Collier T, Birch HL, de Leeuw NH. Journal of Molecular Modeling (2018), (24)5. DOI: 10.1007/s00894-017-3530-6 Instruction video: https://youtu.be/fQVXv8Ge_tg This Java executable jar derives second order bond force constants for bond stretch and bond angle from quantum mechanical Gaussian calculations. The calculations are compatible with the Amber force field family or any force field derived from... -
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PROMOT
A tool for finding functional motifs from aligned protein sequences
PROMOT (version 4.0) is a bioinformatics tool for discovering motifs (in the PROSITE format) from a set of aligned sequences. To run the tool, you need to have Java 8 installed on your system. Download and execute the JAR without any parameters to know about how to use the tool. A sample alignment of 91 protein sequences is also provided in the file "aligned.fasta". A sample run of the tool can be seen by using the following command: java -jar promot4.jar 70 2 n aligned.fasta > output.txt... -
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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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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
A protein contact matrix is 2D representation of the distances between amino acid residues in a 3D protein structure. Protein Contact Map Generator (PCMGen) is a command line tool which takes protein 3D structures (PDB format files) as input and computes contact distances between two chains (from single or two different proteins). These matrix files can be further visualised as Contact Maps using other visualization tools/ programs (like R-heatmaps). Contact Maps can be used to understand... -
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GESPA
Accurately predicts disease association of single nucleotide mutations
... are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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NOTE: developement of this project has moved to GitHub http://github.org/matthuska/biasviz/ BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.
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cmotif
A method for mining conditional phosphorylation motifs
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif... -
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Project provides a set of concurrent building blocks (Java & C/C++) that can be used to develop parallel/multi-threaded applications. Components are grouped into 4 categories: 1.Data Structures 2. Parallel Patterns 3.Parallel functions 4.Atomics and STM
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Autmated Peptide Screening
Screening peptides for MHC and/or MHC-T cell receptor affinity
Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added... -
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l
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Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!! It has a built-in database and contains information about all the physical properties and lets you to search them
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Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
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A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)
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Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.
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