Search Results for "secondary structure prediction source code"
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Showing 15 open source projects for "secondary structure prediction source code"
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Award-Winning Medical Office Software Designed for Your SpecialtyRXNT is an ambulatory healthcare technology pioneer that empowers medical practices and healthcare organizations to succeed and scale through innovative, data-backed, AI-powered software.
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DeepSeek Coder
DeepSeek Coder: Let the Code Write Itself
DeepSeek-Coder is a series of code-specialized language models designed to generate, complete, and infill code (and mixed code + natural language) with high fluency in both English and Chinese. 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... -
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Sample GenLayer project
Includes the boilerplate code for a GenLayer use case implementation
GenLayer Project Boilerplate is an open-source template designed to accelerate the development of decentralized applications on the GenLayer protocol by providing a fully integrated environment that combines intelligent contract logic with a modern frontend interface. It includes a complete working example of a prediction market application, demonstrating how developers can structure, deploy, and test decentralized logic in a real-world scenario. The project integrates both backend contract... -
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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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Alphafold
Open source code for AlphaFold
This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from using this source code or the model parameters should cite the AlphaFold paper. Please also refer to the Supplementary Information for a detailed description of the method. You can use... -
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Alphafold2
Unofficial Pytorch implementation / replication of Alphafold2
To eventually become an unofficial working Pytorch implementation of Alphafold2, the breathtaking attention network that solved CASP14. Will be gradually implemented as more details of the architecture is released. Once this is replicated, I intend to fold all available amino acid sequences out there in-silico and release it as an academic torrent, to further science. Deepmind has open sourced the official code in Jax, along with the weights! This repository will now be geared towards a... -
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Awesome Conformal Prediction
A professionally curated list of awesome Conformal Prediction videos
awesome-conformal-prediction is a curated “awesome list” repository on GitHub collecting high-quality resources related to conformal prediction: tutorials, books, papers, theses, open-source libraries, videos, and other educational material. It is not a software library itself but a directory of resources for those wanting to learn or work with conformal prediction and uncertainty quantification. This exceptional resource is the culmination of my PhD journey in Machine Learning, specializing... -
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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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node2vec
Learn continuous vector embeddings for nodes in a graph using biased R
The node2vec project provides an implementation of the node2vec algorithm, a scalable feature learning method for networks. The algorithm is designed to learn continuous vector representations of nodes in a graph by simulating biased random walks and applying skip-gram models from natural language processing. These embeddings capture community structure as well as structural equivalence, enabling machine learning on graphs for tasks such as classification, clustering, and link prediction.... -
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Crystal Structure Prediction
MOLPAK (MOLecular PAcKing) is used for predicting crystal structures
MOLPAK (MOLecular PAcKing) is a program for the prediction of crystal structures used in both energetic materials and pharmaceutical design. The MOLPAK package, as currently distributed, includes the MOLPAK code, PMIN code, Utilities programs, an interface program and a users guide document. -
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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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A Scalable Multicore Code for RNA Secondary Structure Prediction
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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... -
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The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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DANGLE: A Bayesian inferential prediction method for protein backbone dihedral angles and secondary structure assignments, solely from sequence information, experimental chemical shifts and a database of known protein structures and their shifts.
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