End-to-end deep learning toolkit for predicting protein binding sites and motifs.
☆45Feb 26, 2019Updated 7 years ago
Alternatives and similar repositories for deepRAM
Users that are interested in deepRAM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- CNN architecture for predicting DNA binding sites for Transcription Factors☆53Feb 6, 2019Updated 7 years ago
- ProNA2020: System predicting protein-DNA, protein-RNA and protein-protein binding sites from sequence☆14Aug 7, 2020Updated 5 years ago
- ☆20Jun 10, 2024Updated last year
- BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models☆14Aug 21, 2022Updated 3 years ago
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆27Mar 13, 2023Updated 3 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Visualize structure data from Biotite with PyMOL☆26Mar 16, 2025Updated last year
- Ligand-binding site classification with deep graph neural networks.☆10Sep 24, 2023Updated 2 years ago
- kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengths☆10May 29, 2017Updated 8 years ago
- A hierarchical deep learning framework for ncRNA-protein interaction prediction.☆14Nov 25, 2022Updated 3 years ago
- Major Histocompatibility Complex (MHC) Binding Affinity Prediction☆10Apr 22, 2021Updated 4 years ago
- "Representation Learning of Genomic Sequence Motifs with Convolutional Neural Networks" by Peter K. Koo and Sean R. Eddy☆34Jan 7, 2020Updated 6 years ago
- ☆20Feb 25, 2025Updated last year
- Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.☆18Jun 10, 2022Updated 3 years ago
- A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences☆97Aug 14, 2022Updated 3 years ago
- NordVPN Threat Protection Pro™ • AdTake your cybersecurity to the next level. Block phishing, malware, trackers, and ads. Lightweight app that works with all browsers.
- Sequence-based protein solubility predictor☆11Apr 1, 2020Updated 6 years ago
- Summary statistics for repertoires☆17Feb 1, 2023Updated 3 years ago
- Pytorch implementation of Pocket2Drug: a generative deep learning model to predict binding drugs for ligand-binding sites.☆22May 19, 2022Updated 3 years ago
- Prediction of protein substitution impact using a directional substitution matrix and homolog alignments☆12Oct 25, 2021Updated 4 years ago
- Variational Auto Encoders for learning binding signatures of transcription factors☆14Mar 14, 2024Updated 2 years ago
- protein backbone refinement☆15Sep 12, 2024Updated last year
- Learning Protein Constitutive Motifs from Sequence Data: RBM toolbox☆20Jan 30, 2019Updated 7 years ago
- Perform hyper-parameter tuning, training, testing and prediction with Keras☆44May 29, 2018Updated 7 years ago
- A surface-based deep learning approach for the prediction of ligand binding sites on proteins☆45Apr 22, 2023Updated 2 years ago
- NordVPN Special Discount Offer • AdSave on top-rated NordVPN 1 or 2-year plans with secure browsing, privacy protection, and support for for all major platforms.
- Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.☆16Aug 13, 2019Updated 6 years ago
- ☆15May 22, 2025Updated 10 months ago
- Official repo for paper "AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions"☆17Dec 8, 2024Updated last year
- a toolbox for the manipulation, modelling and analysis of molecular structures☆27Nov 27, 2025Updated 4 months ago
- A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.☆16Jul 25, 2016Updated 9 years ago
- A project to capture biological pathway data from academic papers☆29Mar 24, 2025Updated last year
- The SimSite3D Software tools are designed to quickly search a database of three dimensional structures, in Protein Data Bank format, with…☆11Oct 18, 2018Updated 7 years ago
- A curated list of awesome clonality and tumor heterogeneity resources☆15Jun 25, 2019Updated 6 years ago
- Quantifying the nativeness of antibody sequences using long short-term memory networks☆18Dec 17, 2021Updated 4 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- 🧛 Deep generative models for TCR sequences 🧛☆17Apr 4, 2022Updated 4 years ago
- open toolbox for structural comparison☆13Dec 13, 2018Updated 7 years ago
- Structural space exploration of AlphaFold DB☆12Oct 8, 2021Updated 4 years ago
- iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide …☆196May 23, 2022Updated 3 years ago
- A framework for rapidly mining structural information from the Protein Data Bank☆53Jun 2, 2020Updated 5 years ago
- Code for our paper "Protein sequence design with a learned potential"☆83Sep 8, 2023Updated 2 years ago
- Predict the boundary of transcript start and end from RNA-seq reads alignment☆11Feb 13, 2017Updated 9 years ago