Search Results for "protein" - Page 3
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Showing 405 open source projects for "protein"
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ENPG
A tool to extract potential neuropeptides from protein sequence data.
This tool is intended to extract potential neuropeptide regions from protein sequence data. The currently available version is dedicated to extract peptides that shows the structural hallmarks of cnidarian neuropeptides (C-terminal amidation, proline at N-terminus and pyro-Glutamate). The output FASTA file can be used as a target data set for peptide-spectrum matching to effectively narrow search space for highly sensitive peptide identifications. -
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JCVI VIGOR
Viral Genome ORF Reader
VIGOR (Viral Genome ORF Reader) is a perl application to predict protein sequences encoded in viral genomes. VIGOR determines the protein coding sequences by sequence similarity searching against curated viral protein databases. Please see the wiki to see list of all supported viruses. This work has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under... -
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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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CUDASW++: Smith-Waterman Algorithm
The fastest Smith-Waterman protein database search algorithm on GPUs
CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html -
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altanalyze
Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as well... -
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CompleXChange
differential analysis of combinatorial protein complexes
The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z. -
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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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comer
Protein remote homology search tool
COMER is a protein sequence alignment tool designed for protein remote homology detection. It accepts a multiple sequence alignment as input and converts it into the profile to search a profile database for statistically significant similarities. COMER is licensed under the GNU GP License, version 3. Please find its archive file, download and extract it with the command "tar -zxf <archive-name>", and refer to the README file for instructions on how to use the software. Funding: This work... -
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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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AUTOMINv1.0
Automation for Minimization of Protein Data Bank Files, version 1.0
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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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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
hppRNA package is dedicated to the RNA-Seq analysis for a large number of samples simultaneously from the very beginning to the very end, which is formulated in Snakemake pipeline management system. It starts from fastq files and will produce gene/isoform expression matrix, differentially-expressed-genes, sample clusters as well as detection of SNP and fusion genes by combination of the state-of-the-art software. The first version handles protein-coding genes, lncRNAs and circRNAs and includes... -
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ProDistiller
A software to perform quality control at protein level
ProDistiller is a quality-control tool based on the results of PepDistiller. ProDistiller focuses on QC at protein level and protein inference. Using PepDistiller and ProDistiller, you can obtain the QC results at both PSM and protein levels easily. -
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PTM-X
a solfware for predicting posttranslational modification cross-talk
The PTM-X (PTM cross-talk) project is a freely available bioinformatics software platform that allows to calculate the features of PTM pairs and the posterior probabilities of being cross-talk pairs. The prediction model is a naive Bayse classifier that integrats five features: protein sequence distance, tertiary structural distance, co-location in a disordered region, residue co-evolution, and modification co-evolution. An online tool is also available at http://bioinfo.bjmu.edu.cn/ptm-x/. -
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PF_HP
Prediction of proteinfolding in 2D HP model
... einen Cappuccino: Bitcoin: 1HqrdnfQgi9B4LW8UEvLAwh7X5gXPCoQ5B Litecoin: Lbo2jxD85ymyq5167r7yFVZkEr73F2h44B Paypal: paypal.me/GerritLeder Credits ====== Principle Investigator -------------------------- Gerrit Leder: protein folding algorithm design and testing, and initial implementation in Eiffel. Eiffel Consultant --------------------- Finnian Reilly: Eiffel code optimization and parallel processing adaptation. www.hex11software.com finnian at eiffel hyphen loop dot com -
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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/projects... -
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POVME (POcket Volume MEasurer) is a program for calculating the volumes of macromolecular (e.g. protein) binding pockets. In essence, POVME floods a pocket-encompassing region with equidistant points, removes those points that are near receptor atoms, and calculates the volume from the remaining points. NOTE: The latest version of POVME is now available at http://git.durrantlab.com/jdurrant/POVME. Versions on SourceForge are not up to date.
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Grinn
graph database and R package for omic data integration
http://kwanjeeraw.github.io/grinn/ -
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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.
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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 -
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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. -
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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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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...
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and... -
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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.