Search Results for "protein" - Page 4
Sort By:
Showing 363 open source projects for "protein"
View related business solutions-
Boost application security and continuity with SKUDONET ADC, our Open Source Load Balancer, that maximizes IT infrastructure flexibility. Additionally, save up to $470 K per incident with AI and SKUDONET solutions, further enhancing your organization’s risk management and cost-efficiency strategies.
-
HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
-
1
Grinn
graph database and R package for omic data integration
http://kwanjeeraw.github.io/grinn/ -
2
OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
-
3
PSOVina 2.0
The Hybrid Particle Swarm Optimization for Protein-Ligand Docking
A fast docking tool based on the efficient optimization algorithm of Particle Swarm Intelligence and the framework of AutoDock Vina. Based on the initial PSO implementation, our PSOVina method has undergone several important improvements to enhance the docking accuary and achieve remarkable efficiency as compared to the original AutoDock Vina. https://cbbio.online/software/psovina/index.html -
4
PPICompare
detection of rewiring events in protein interaction networks
PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x. -
AlertBot monitors your website's full functionality around the clock so you can focus your time on more important things.
-
5
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...
-
6
FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information. For SNP data, it also predicts the effect of SNPs in the protein coding regions on the codons involved and marks SNPs potentially affecting start and stop codons and splice sites. It also identifies features of user’s interest, such as genes, or biomarkers in the vicinity of the features...
-
7
XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
8
chops
Convex Hull Of Protein Surface
This program will calculate all k-th convex hulls of protein surface when input a protein pdb file (pdb format), it is supplied in source code form along with the required data files and run under the windows/linux. -
9
ASBAAC
salt-bridge and aromatic-aromatic analysis
The software ASBAAC, easily calculate salt-bridge and aromatic-aromatic contact of multi-chain protein complex. ASBAAC is written on AWK programming language and this software is run from C shell Unix prompt in 32-bit CYGWIN OS . -
Don’t settle when it comes to managing your clients’ IT infrastructure. Exceed their expectations with ConnectWise RMM, our MSP RMM software that provides proactive tools and NOC services—regardless of device environment. With the number of new vulnerabilities rising each year, smart patching procedures have never been more important. We automatically test and deploy patches when they are viable and restrict patches that are harmful. Get better protection for clients while you spend less time managing endpoints and more time growing your business. It’s tough to locate, afford, and retain quality talent. In fact, 81% of IT leaders say it’s hard to find the recruits they need. Add ConnectWise RMM, NOC services and get the expertise and problem resolution you need to become the advisor your clients demand—without adding headcount.
-
10
AC-DIAMOND is a DNA-protein aligner. The source code of AC-DIAMOND can be found here: https://github.com/Maihj/AC-DIAMOND
-
11
GAPE
proteogenomic analysis software
... of annotated genes, identification of previously unidentified genes, protein level identification of alternative spliced variants and SAAV, biological interpretation, and global PTM discovery. -
12
Protein Microarray Analyser
Protein microarray data processing and normalization
The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. -
13
idwtree
Assigns orthologs using a phylogenetic tree
Protein BLAST analysis finds all homologs of a protein; however, for many analyses, it is important to identify orthologs in different species (e.g. homologs that derive from the same ancestral sequence). The program idwtree aid in this analysis by assigning 'group' identity in phylogenetic trees containing reference sequences as markers. The standard workflow idwtree was intended to analyze: 1. BLAST protein sequence of interest against organism(s) of interest. 2. Download all... -
14
IPAS for protein sequences
multiple alignment algorithm for protein sequences
IPAS is a new and practial protein multiple sequence alignment algorithm based on iterative progresive alignment algorithm Assessed on BAliBASE 3.0, PREFAB 4.0, SABMARK 1.65, and OXBENCH, MSAProbs achieves the statistically highest alignment accuracy, compared to ClustalW 2.0.10, MAFFT 6.717( using L-INS-i with --maxiterate = 1000), MUSCLE 3.8.31, ProbCons 1.12, and Probalign 1.3. -
15
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.
-
16
GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
17
mapDIA
Model-based Analysis of quantitative Proteomics data in DIA-MS
mapDIA performs essential data preprocessing, including novel retention time-based normalization method and a sequence of peptide/fragment selection steps, and more importantly, hierarchical model-based statistical significance analysis for multi-group comparisons under representative experimental designs. The advanced modelling technique also allows the user to incorporate relational information such as existing network data or protein-peptide mapping, enabling module-oriented analysis... -
18
Application to optimize DNA sequences coding protein to put in in the different organizm (f.e. human protein in E.Coli). It proposes the optimal cutting places to connect many shorter fragments into bigger one using ligaze.
-
19
-
20
SILVER
SILVER: An efficient tool for stable isotope labeling quantification
With the advance of experimental technologies, different stable isotope labeling methods have been widely applied to quantitative proteomics. Here, we present an efficient tool, named SILVER for processing the stable isotope labeling mass spectrometry data. SILVER implements novel methods for quality control of quantification at spectrum, peptide and protein levels respectively. Several new quantification confidence filters and indices are used to improve the accuracy of quantification results... -
21
MatQuantify
An image processing tool
... deviation of intensities. Using MatQuantify, we studied the effect of knocking down the protein clathrin heavy chain (CHC) on the mitotic spindle. We analysed 217 microscopy images of untreated metaphase cells, 172 images of metaphase cells transfected with small interfering RNAs targeting the luciferase gene (as a negative control), and 230 images of metaphase cells depleted of CHC. Using the quantified data, we trained 23 supervised machine learning classificatio -
22
cfPred
Chou & Fasman algorithm implemented using C language.
Chou & Fasman algorithm implemented using C language. It is a CUI tool used for protein secondary structure prediction. -
23
Neuro
The Neuro crypto currency
... as GoogLeNet Inception and Microsoft ResNet. At further stages of the work, we adapt the neural networks to calculate molecular interactions in protein environments. Our system will help to look for new types of drugs for cancer, Alzheimer's and other serious problems of modern medicine. We plan to make a serious contribution to the increase of human life expectancy. -
24
MSqBAT
Label-free protein quantification for LC-MS
MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data. It was developed in the lab of Dr. Christoph Rösli at the Heidelberg Institude for Stem Cells and Experimental Medicine (HI-STEM) and the German Cancer Research Center (DKFZ). It’s main features are 1) Label-free, MS1-based quantification 2) Support both LC-MALDI-MS- as well as LC-ESI-MS data 3) Supports both GeLC-MALDI-MS- and GeLC-ESI-MS data 4) Convenient, graphical... -
25
HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.