Search Results for "protein"
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Showing 519 open source projects for "protein"
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Make-A-Video - Pytorch (wip)
Implementation of Make-A-Video, new SOTA text to video generator
Implementation of Make-A-Video, new SOTA text to video generator from Meta AI, in Pytorch. They combine pseudo-3d convolutions (axial convolutions) and temporal attention and show much better temporal fusion. The pseudo-3d convolutions isn't a new concept. It has been explored before in other contexts, say for protein contact prediction as "dimensional hybrid residual networks". The gist of the paper comes down to, take a SOTA text-to-image model (here they use DALL-E2, but the same learning... -
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code"... -
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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Developed with Synchronized functioning of Python and Batch scripts - Compatible on Windows - Accepted on Journal of Computational Chemistry - DOI: 10.1002/jcc.27390 -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Combinatorial Molecule Generation - Integerated with Molecule Drawing Tool - JSME Editor -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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iem-configurator
Configurator for protein substitutes
This configurator helps you to calculate optimal dosage of protein substitutes. -
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC... -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
... and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes. -
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OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis... -
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AutoDockParser
A tool for efficient processing of Docking results
... a time-consuming and apparently mundane task. Manual processing involves dependency on various external software. AutoDock Parser offers automatic post-processing of the docking results obtained from AutoDock Suit. AutoDock Parser is a user-friendly tool aimed to minimize the efforts in the post-processing of docking results. It enables the user to create protein-ligand complexes from the input DLG/PDBQT files in a single step. -
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PSSPT
PSSPT (Protein Secondary Structure Prediction Tool)
PSSPT (Protein Secondary Structure Prediction Tool) Please, visit our GitHub page for more detail. -
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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comer2
COMER2, cross-platform software for protein remote homology search
The COMER method based on sequence profile-profile comparison is one of the most sensitive and accurate computational tools developed for protein alignment and homology search. COMER version 2.1 (COMER2) represents one of the fastest implementations of calculations for sensitive protein homology search. High COMER2 performance is achieved by harnessing the power of the Graphics processing unit (GPU). Hence, a GPU is expected to be installed on the system. The files include the compressed... -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab... -
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ExtAncSeqMEGA is a program to extract ancestral DNA sequences that have been calculated by MEGA. ExtAncSeqProt is a program to extract ancestral PROTEIN sequences that have been estimated by MEGA. See the ReadMe file for details and documentation
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. Enhanced sampling...
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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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trilat-umn
Using FRET distances to trilaterate the location of a FRET acceptor
This software performs trilateration using an arbitrary number of donor sites and FRET distances with the aim to locate the position of a FRET acceptor in a protein structure. Our trilateration approach takes into account Gaussian distance distributions as fitted to the FLT-FRET measurement for each donor position. The normalized sum of the distance distributions from all of the donor sites to one acceptor is generated as a probability map describing the acceptor’s location. This volumetric map... -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred from... -
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
This GUI app allows users to input biological sequences, either manually or by loading from a file. It supports DNA, RNA, and Protein sequences. Users can retrieve various information about the input sequence, such as nucleotide or amino acid frequency, GC content, reverse complement, transcription, translation, amino acid molecular weight, isoelectric point, and open reading frames. Users can save the output information to a text file and clear the output section for a clean slate... -
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Shetti 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. Shetti is an automated and user-friendly tool to manipulate protein or gene sequences, GenBank and UniProt raw files, and transform them to human-readable format. The tool is developed to help the experimental biologists, without prior programming skills, to manipulate sequences quickly, easily and precisely. The methods...
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LibreCalories
Libre version of the many costly nutrition and calorie counting apps.
LibreCalories is a libre version of the many costly nutrition and calorie counting apps out there. While still in its early stages, LibreCalories is a step forward towards making nutritional knowledge freely accessible, and giving all an opportunity to engage in a healthier lifestyle. To access the source code, report an issue, or make a contribution of any kind, head on over to the project's Git at CodeBerg: https://codeberg.org/powerchimp7/librecalories/ For contact information, head... -
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Biochemistry
Compares serum biochemistry parameters in selected animals
Biochemistry compares your serum biochemistry parameters of animals with one's reference values (Kaneko et al, 2008) and can save laboratory card for tested parameters. Cat, dog, pig, cow and horse are included -
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics research... -
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aramultiomics
A toolkit for studying protein-protein/nucleic acid interaction
araMultiOmics consisted of seven modules where each module was created based on existing databases and software for studying protein binding sites/open chromatin regions, DNA-TF bonding profile, etc