Integer programming based prediction of RNA secondary structures with pseudoknots
☆23Jul 18, 2026Updated this week
Alternatives and similar repositories for ipknot
Users that are interested in ipknot are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Parallel solution for local RNA secondary structure analysis☆12Feb 14, 2023Updated 3 years ago
- Physics Informed Neural Networks (PINNs) code to solve the 3D Poisson-Boltzmann equation.☆17Mar 31, 2025Updated last year
- Eterna100-V2 benchmarking results and scripts☆14May 19, 2026Updated 2 months ago
- RNAView identifies base pairs that are formed in nucleic acid structures and classifies them according to the system of Leontis and Westh…☆20Jul 11, 2024Updated 2 years ago
- DyNoPy☆11Sep 5, 2024Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome a…☆18May 9, 2023Updated 3 years ago
- Centroid RNA package☆20Oct 12, 2020Updated 5 years ago
- Create force-directed graphs of RNA secondary structures.☆112Jun 6, 2020Updated 6 years ago
- Finds the optimal stem configuration of an RNA sequence using the LeapHybridCQMSampler.☆17Oct 31, 2023Updated 2 years ago
- Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energ…☆20Apr 3, 2021Updated 5 years ago
- ☆40Dec 15, 2023Updated 2 years ago
- bpRNA: Large-scale Annotation and Analysis of RNA Secondary Structure☆52Nov 23, 2023Updated 2 years ago
- 🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs …☆185Apr 8, 2026Updated 3 months ago
- Linear-Time Approximation of RNA Folding Partition Function and Base Pairing Probabilities☆36May 24, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Jul 28, 2022Updated 3 years ago
- ☆56Nov 14, 2025Updated 8 months ago
- Simulation code for the prediction of RNA structures.☆14Jan 21, 2025Updated last year
- Twitter retrosynthesis bot☆13Jul 10, 2022Updated 4 years ago
- The ViennaRNA Package☆419Feb 24, 2026Updated 4 months ago
- ☆12May 3, 2025Updated last year
- Modelling RBP binding preferences to predict RPB binding sites☆11Aug 11, 2023Updated 2 years ago
- init commit☆16Oct 31, 2023Updated 2 years ago
- Deconvolution of RNA Alternative COnformations☆15Jun 24, 2026Updated 3 weeks 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.
- Perl scripts for analysis RIC-seq data☆11Feb 6, 2020Updated 6 years ago
- SHAPE-guided RNA structural homology search☆12Aug 12, 2025Updated 11 months ago
- To be readable without enhancing english power.☆10Jul 22, 2020Updated 5 years ago
- ☆13May 26, 2022Updated 4 years ago
- State of the art software for RNA sequence design. The first to solve the Eterna benchmark!☆16Jul 17, 2024Updated 2 years ago
- Program to calculate SDPs using Noisy intermediate scale quantum (NISQ) computers.☆12Feb 3, 2025Updated last year
- SPOT-1D-LM: Reaching Alignment-profile-based Accuracy in Predicting Protein Secondary and Tertiary Structural Properties without Alignmen…☆11Feb 1, 2024Updated 2 years ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Oct 27, 2022Updated 3 years ago
- Inverted Repeats Finder: a program to analyze DNA and RNA sequences☆22Feb 21, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Soccer Trajectory Prediction Competition☆16Aug 28, 2025Updated 10 months ago
- Deep transformer for predicting interchain residue-residue distances of protein complexes☆14Mar 19, 2024Updated 2 years ago
- Analyse Nucleic Acids Structure and Simulations with baRNAba☆59Mar 20, 2024Updated 2 years ago
- Some tutorials to help people learn how to program the D-Wave quantum computer.☆13Oct 4, 2018Updated 7 years ago
- SVG collection of lab equipment☆13Nov 28, 2022Updated 3 years ago
- Rapid mining of RNA structure motifs from profiling data.☆14Oct 20, 2021Updated 4 years ago
- Python implementation of the FR3D software for searching and annotating RNA 3D structures☆24Jul 1, 2026Updated 2 weeks ago