Search Results for "proteins"
Sort By:
Showing 94 open source projects for "proteins"
View related business solutions-
Outgrown Windows Task Scheduler?Windows Task Scheduler wasn't built for complex, cross-platform automation. Get a free diagnostic that shows exactly where things are failing and provides remediation recommendations. Interactive HTML report delivered in minutes.
-
Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
-
1
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. -
2
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 anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
3
UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
4
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. -
Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
-
5
PANDA
A comprehensive and flexible quantification tool for proteomics data
...First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels 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. -
6
TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
7
NOVA
Analysis and visualization of complexome profiling data.
...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, image export, and automatic file format recognition support intuitive handling for biologists. Giese, et al. NOVA: a software to analyze complexome profiling data. Bioinformatics, 2015, 31(3): 440-441 -
8
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.
-
9
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).
-
Dun and Bradstreet Connect simplifies the complex burden of data managementThe amount, speed, and types of data created in today’s world can be overwhelming. With D&B Connect, you can instantly benchmark, enrich, and monitor your data against the Dun & Bradstreet Data Cloud to help ensure your systems of record have trusted data to fuel growth.
-
10
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. -
11
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 interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness. ... -
12
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/projects/opengrowth/files). ... -
13
PPLine
SNP calling, annotation and gene/transcripts expression quantification
...PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
14
PanOCT
Pan-genome Ortholog Clustering Tool
...Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters. -
15
rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. -
16
irayMol
Molecular visualization
Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch. -
17
datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
...The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. D71, 1347–1350 -
18
Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
-
19
DORY
For mining KASH proteins (SUN domain-interacting proteins)
....*** Please see the following publication for detail: Zhou X, Graumann K, Wirthmueller L, Jones JDG, Meier I (2014) Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants. The Journal of Cell Biology 205(5):677-692. http://jcb.rupress.org/content/205/5/677.full Please see other useful tools for biology research: https://sourceforge.net/projects/cloversystem/?source=directory -
20
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 user interface Acknowledgements The development of MSqBAT is kindly supported by YourKit Java Profiler. -
21
SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
...Sensitivity is gained by repeatedly running the HMM gene predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use. -
22
KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
-
23
Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with... -
24
PingPongPro
Find ping-pong signatures like a pro
...Please refer to: https://github.com/suhrig/pingpongpro Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs, predominantly active in the germ line. There, they limit the detrimental effect of transposons on the genome. They do so by forming a complex with Piwi proteins. The complex binds and then cleaves mRNA molecules of active transposons. The resulting mRNA fragments induce the production of more piRNAs, thus reinforcing the anti-transposon response in a feed-forward loop called the "ping-pong cycle". A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. ... -
25
NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
...If you use the NGS TOOLBOX you for publication purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313.
