Search Results for "proteins"
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Showing 118 open source projects for "proteins"
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KrakenD is a high-performance API Gateway optimized for resource efficiency, capable of managing 70,000 requests per second on a single instance. The stateless architecture allows for straightforward, linear scalability, eliminating the need for complex coordination or database maintenance.
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wger
Self hosted FLOSS fitness/workout, nutrition and weight tracker
... in the same program. Create your personal diet plan by creating as many meals with as many different ingredients as you need. The application will calculate the nutritional values (total energy, proteins, carbohydrates, etc.) of the entire plan and of each of the meals. Enter the weights and reps you've done for each exercise to generate diagrams that let you see at a glance how well you're doing. Of course, the raw numbers are still accessible. -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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rafah
Random Forest Assignment of Hosts
One fundamental question when trying to describe viruses of Bacteria and Archaea is: Which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), which outperformed other methods for virus-host prediction. Our rationale was that the machine could learn the associations between genes and hosts much more efficiently than a human, while also using the information contained in the hypothetical proteins. Random forest... -
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NifFINDER
A preditor of Nif proteins
Tool developed in MATLAB to identify the set of proteins encoded by the nifs genes (which are called Nifs). Niffinder identifies up to 24 Nifs - For each Nif protein an Artificial Neural Network (ANN) was built. -
Take away the pain and hassle associated with applicant recruitment, hiring, and onboarding with ApplicantStack. Designed for HR professionals and recruiters, ApplicantStack helps streamline the recruiting and onboarding processes to improve productivity and reduce costs. ApplicantStack provides a complete toolkit that includes tools for posting, launching, and advertising jobs, assessing and managing candidates, collaborating with teams, centralizing information for quick hiring and onboarding, and more.
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MCE - Marching Cube ELD
Crystallographic software for displaying voxel maps - electron density
MCE is an crystallographic experimental program for 3D and 2D electron density map visualization. The software is mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well. Download the installation file (default download) or find in "Files" the zip-file with instant copy of the program which does not require the installation. -
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Shetti-Motif can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Short linear motifs / domains (SLiM) facilitate the functions and interactions of the proteins. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. ShettiMotif, which is an interactive tool to (i) searches for motifs containing repeated...
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PANDA
A comprehensive and flexible quantification tool for proteomics data
... of spectra, peptides and proteins, PANDA works out a few quantitative filters and new scores for quantification confidence. Third, PANDA is designed for processing proteomics big data in parallel. -
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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DeeProtGO
DeeProtGO is a deep learning model for predicting GO terms of proteins
This project contains the source code of DeeProtGO as well as an example of its use when predicting GO terms of the biological process sub-ontology for eukaryotic proteins. -
Our robust pre-built connectors and our no-code, drag-and-drop interface makes it easy and fast to automatically sync vendors, invoices, and invoice payment data between Tipalti and your ERP or accounting software.
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MS-Helios
MS-Helios: A Circos wrapper to visualize multi-omic datasets
Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challenge to data analysis and visualization, requiring methods to reduce dimensionality and represent the data in a compact way. To provide a more holistic view, we recently introduced circular proteome maps (CPMs). However, the CPM construction requires prior data transformation... -
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DisPC – a large scale disorder prediction and analysis tool which is a meta-predictor in one hand and also performs a proteome wide analysis of function, binding region prediction and evolutionary conservation analysis of the intrinsically disordered proteins (IDPs). DisPC is tested in several bacterial and fungal genomes for detailed genome wide analysis of IDPs. This pipeline can be used for large scale identification and characterization of IDPs in different domains of life.
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NOVA
Analysis and visualization of complexome profiling data.
NOVA is a program designed to analysis complexome profiling data (Heide et al., 2012). A graphical user interface (GUI) provides various visualization tools, such as heat maps and 2D plots. Several hierarchical clustering algorithms (e.g., single linkage, average linkage, Wards linkage), different distance measures (e.g., Euclidean distance, Manhattan distance, Pearson distance), and various normalization techniques are implemented. Many additional functions like zooming, searching for proteins... -
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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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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esPOS
A predictor to identify essential protein from PPI network
Predicting essential proteins from protein-protein interactions using order statistics -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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This is a Python-based efficient implementation of several semantic similarity measures. The target is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology (GO).
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DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein... -
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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments. The details can be found in the original publication "OpenGrowth: an automated and rational algorithm for finding new protein ligands" (J. Med. Chem., http://dx.doi.org/10.1021/acs.jmedchem.5b00886). To use OpenGrowth, you will need OpenGrowth_1.0.zip and Resources_1.0.2.zip that can be found by clicking on the Files menu in the horizontal bar at the top (https://sourceforge.net... -
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We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors. The estimated protein clusters form regulatory modules in different chromatin states, which help explain how proteins work together in regulating gene expression. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins...
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PROPAB
PROPensity for Alpha and Beta
PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins Authors: Rifat Nawaz UL Islam1, Chittran Roy2, Parth Sarthi Sen Gupta3, Debanjan Mitra2, Sahini Banerjee4 and Amal Kumar Bandyopadhyay2* 1Department of Zoology, The University of Burdwan, West Bengal, 713104, India 2Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India 3Department of Chemistry, IISER, Berhampur, Odisha, 760010, India 4Department... -
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NMRspectroscopy is a package providing ease in installing some popular tools regarding proteins' analysis. It also provides a GUI interface for the tools.
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VacSol
An in slico pipeline to predict potential therapeutic targets
... to identify putative therapeutic targets against the infectious agents. In current study we have developed an in silico, multi-threaded, configurable and scalable pipeline employing subtractive-reverse vaccinology analysis technique and named it VacSol (https://sourceforge.net/projects/vacsol/). The principle objective of the VacSol development is to screen out genes/proteins from microbial genome/proteome that could be employed as potential therapeutic targets -
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QPROT is a software for differential protein expression using spectral count and intensity data. It also accounts for independent samples and paired samples. The input data should be rolled up to proteins before analysis. Extension to peptide level analysis is in progress.
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TMoLiC
Population Density Calculation
This project will help researchers to implement Population Density Approach in order to find the The Most Likely Configuration among all possible using TMoLiC software. This approximation was created to establish initially the Asp Dyad protonation state of Aspartyl Proteases. However, the concept can be expand to proteins in general to aboard conformational changes or protonation state problems. For more deatils regarding Population Density concept, please read: https://doi.org/10.1080...