Search Results for "secondary structure"
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Showing 37 open source projects for "secondary structure"
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RedisJSON
RedisJSON - a JSON data type for Redis
RedisJSON is a Redis module that implements ECMA-404 The JSON Data Interchange Standard as a native data type. It allows storing, updating and fetching JSON values from Redis keys (documents). -
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DeepSeek Coder
DeepSeek Coder: Let the Code Write Itself
...The models are trained from scratch on a massive corpus (~2 trillion tokens), of which about 87% is code and 13% is natural language. This dataset covers project-level code structure (not just line-by-line snippets), using a large context window (e.g. 16K) and a secondary fill-in-the-blank objective to encourage better contextual completions and infilling. Multiple sizes of the model are offered (e.g. 1B, 5.7B, 6.7B, 33B) so users can trade off inference cost vs capability. The repo provides model weights, documentation on training setup, evaluation results on common benchmarks (HumanEval, MultiPL-E, APPS, etc.), and inference tools. -
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Here, we developed a topology-driven scaffold design model, EpiTopoFold, that systematically explores protein secondary-structure arrangements to identify optimal scaffolds for discontinuous epitope segments.
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Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
R2R is a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules. R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and... -
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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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jynew
Heros of Jin Yong 3D Remastered
Heros of Jin Yong 3D Remastered is an open world RPG game with turn-based battle system. It is a non-profit game project which remastered the classic game Legends of Kim-Yong. This project supplies a framework for MODs and secondary development. You can play it on PC, Mac, mobile platform(or other supported platform). -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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Weinberg-CMfinder
Predict and score RNA secondary structures
The CMfinder package is a suite of programs with two main purposes: (1) the cmfinder program infers an alignment and consensus secondary structure of an RNA, using unaligned sequences as input. (2) other tools score alignments to indicate evidence of RNA secondary structure within the alignment. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic model. hmmpair assigns a score based on evidence of covariation that is supported by sequence conservation. ... -
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packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
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RNAfdl
RNA force directed layout
RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings. -
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Spectral-SpecPro
Spectral - software for manipulating optical spectroscopy data
...Spectral takes files produced by Jasco instruments (uv-vis absorbance, fluorescence, circular dichroism readings as a function of wavelength, temperature, or time) and facilitates basic operations such as unit conversion (CD spectra), conversion into the format taken by CDPro (estimation of secondary structure; CD spectra), scatter correction (absorbance spectra), smoothing, re-sampling of the x-axis, and generic combination (sum, product, average, standard deviation) of multiple curves. Spectral-SpecPro is based on earlier software written by Stephen R Martin (MRC-NIMR London NW7 and Francis Crick Institute London NW1). -
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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. -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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Multiple Sequence Alignment using DP
Dynamic Programming (DP) is widely used in Multiple Sequence Alignment
...The similarities may reveal evolutionary history and are clues about common biological functions of the sequences. The information of similarity and difference can then be used to predict the secondary or tertiary structure of new sequences and to find the relationships between sequences. MSA is also often used for constructing evolutionary trees from DNA sequences and for analyzing the structures to help in designing new proteins. Usually, to solve an MSA problem is to find an alignment of multiple sequences with the highest score based on a given scoring criterion among sequences. -
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RNAstructure
Predict and analyze RNA secondary structures.
This is a software package for the analysis and prediction of RNA secondary structure. -
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FRETtranslator
Translate smFRET trajectories into RNA secondary strucutures
FRETtranslator is a frame work that allows you to predict a sequence of RNA seondary structure transitions for a given smFRET trajectory. At its core it uses Viterbi-decoding. FRETtranslator combines smFRET data with RNA secondary structure predictions and RNA 3D structure sampling. As such it relies on input from additional software for RNA secondary structure and 3D structure predictions. -
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Protein Contact Matrix Generator
Command line application to generate contact matrix from proteins (3D)
...Contact Maps can be used to understand proteins' : 1. Secondary structures 2. Conformational arrangements 3. Surface interactions -
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Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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ReArch Database Project
Code Repository for the Recursive Relational Archaeological DBMS
The Recursive Relational Archaeological Database (ReArch) is a data management platform that preserves the practical configuration that data tables provide, while relaxing the strict, attribute-based model that so characterized modern databases. The schema consists of an inherently recursive and extensible structure that can incorporate heterogeneous observations and analyses into a common framework in order to evaluate their commensurability. In this manner, ReArch provides a simple platform for analyzing and formally expressing the chains of qualifications and associations that fundamentally characterize excavation contexts, artifact descriptions, geographical information, and the secondary and tertiary materials analyses derived from archaeological materials. ... -
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SABLE is a public domain package for structural bioinformatics that can be used to predict from amino acid sequence secondary structure and solvent accessibility profiles in proteins (see Adamczak, Porollo and Meller, Proteins 56, 2004).
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A Scalable Multicore Code for RNA Secondary Structure Prediction
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GLProbs
GLProbs: Aligning multiple sequences adaptively
...We have also evaluated the practicability of the alignments of GLProbs by applying the tool to three biological applications, namely phylogenetic trees construction, protein secondary structure prediction and the detection of high risk members for cervical cancer in the HPV-E6 family, and the results are very encouraging. -
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RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
