Direct coupling analysis software for protein and RNA sequences
☆61Jul 21, 2025Updated 11 months ago
Alternatives and similar repositories for pydca
Users that are interested in pydca are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RNA Structural Bioinformatics Crash Course & Data Science in Python☆14Oct 19, 2022Updated 3 years ago
- Pseudo Likelihood Maximization for protein in Julia☆52May 15, 2025Updated last year
- Evolutionary couplings from protein and RNA sequence alignments☆309Apr 20, 2026Updated 2 months ago
- Inference of couplings in proteins and RNAs from sequence variation☆124Jan 21, 2023Updated 3 years ago
- ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence☆14Aug 7, 2020Updated 5 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module☆23Jan 27, 2022Updated 4 years ago
- Boltzmann machine learning for Potts models of biological data☆13Jul 24, 2024Updated last year
- Mutation effects predicted from sequence co-variation☆76Sep 3, 2017Updated 8 years ago
- A platform to do RNA science☆28Mar 7, 2021Updated 5 years ago
- Fully convolutional neural networks for protein residue-residue contact prediction☆44Mar 25, 2019Updated 7 years ago
- Visualization, comparison, and analysis of RNA secondary structures via a cross-platform GUI☆18May 19, 2025Updated last year
- Deep residual neural network for protein contact/distance prediction developed by Xu group☆79Sep 13, 2020Updated 5 years ago
- Python tool for the discovery of similar 3D structural motifs across protein structures.☆36Nov 18, 2023Updated 2 years ago
- Explore protein fold space with deep generative models☆16Aug 5, 2024Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Centroid RNA package☆20Oct 12, 2020Updated 5 years ago
- Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learni…☆37Apr 3, 2021Updated 5 years ago
- DomainMapper is a parser for hmmscan full output files built centrally around ECOD domain definitions. Users can optimize DomainMapper's …☆13Dec 13, 2023Updated 2 years ago
- Python package for handling IHM mmCIF and BinaryCIF files☆18Jun 25, 2026Updated last week
- QRNAS: Quick Refinement of Nucleic Acid Structures☆18Apr 30, 2025Updated last year
- Autoregressive networks for protein☆38Feb 27, 2025Updated last year
- A dataset for training and benchmarking deep learning models for RNA structure prediction☆67May 8, 2026Updated last month
- Prepare topology and coordinate file for CG models in Genesis.☆13May 14, 2026Updated last month
- Graphical Representation of Ancestral Sequence Predictions☆14Mar 6, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Universal framework for physically based computational protein design☆36Aug 19, 2023Updated 2 years ago
- C-library for calculating Solvent Accessible Surface Areas☆196May 31, 2026Updated last month
- Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.☆114Nov 8, 2023Updated 2 years ago
- A Python Package for Protein Dynamics Analysis☆549Jun 22, 2026Updated last week
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆38Jul 25, 2024Updated last year
- AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By add…☆120Jun 3, 2026Updated last month
- NLP for Proteins - A paper collection☆13Sep 10, 2020Updated 5 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- ☆10Nov 10, 2023Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Collection of Python scripts to setup and run simulations with OpenMM☆17May 22, 2020Updated 6 years ago
- Code for running BinderFlow☆66Jun 22, 2026Updated 2 weeks ago
- ProtT5 (Transformer) embeddings used for residue wise disorder prediction in proteins☆11Mar 11, 2024Updated 2 years ago
- Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/arch…☆11Apr 6, 2023Updated 3 years ago
- ☆64Dec 10, 2025Updated 6 months ago
- Basic RNA 3D structure comparison metrics in RNA-Puzzles, including INF, DI and RMSD. It also includes `RNA_normalizer` tool in pdb_utils…☆27Dec 3, 2024Updated last year
- GraphSite: protein-DNA binding site prediction using graph transformer and predicted protein structures☆62Aug 3, 2024Updated last year