The SimSite3D Software tools are designed to quickly search a database of three dimensional structures, in Protein Data Bank format, with protein-ligand binding sites to determine which binding sites in the database have steric and chemical similarities to the query binding site.
☆11Oct 18, 2018Updated 8 years ago
Alternatives and similar repositories for SimSite3D
Users that are interested in SimSite3D are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The software for modeling the 3D structure of a genome using Hi-C chromosome conformation capturing data☆11Feb 9, 2018Updated 8 years ago
- ☆10Nov 22, 2022Updated 3 years ago
- Predicting Protein – Ligand Interaction by using Deep Learning Models☆11Nov 13, 2018Updated 7 years ago
- DTMOL: a diffusion transformer model for target-based molecular docking☆10Jun 8, 2026Updated 4 months ago
- Ligand binding site prediction and virtual screening☆12Oct 26, 2018Updated 8 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- ☆12Jun 3, 2019Updated 7 years ago
- A heterogeneous OpenCL implementation of QuickVina2☆19Jan 7, 2023Updated 3 years ago
- A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.☆12Oct 20, 2019Updated 7 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆46Mar 13, 2023Updated 3 years ago
- Ligand-binding site classification with deep graph neural networks.☆10Sep 24, 2023Updated 3 years ago
- A repository to keep code for interaction frequency work going forwards.☆11Mar 21, 2022Updated 4 years ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆20Jun 3, 2025Updated last year
- Use AutoDock for Ligand-based Virtual Screening☆23Aug 18, 2024Updated 2 years ago
- ☆11Aug 7, 2023Updated 3 years ago
- 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.
- Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at th…☆10Aug 20, 2026Updated 2 months ago
- ☆11Aug 5, 2020Updated 6 years ago
- ☆11Nov 26, 2025Updated 11 months ago
- Gigabase: Synthetic Biology Cell Modeling Project☆19Nov 3, 2013Updated 12 years ago
- Neural network for predicting amino acid sequences from protein conformations☆10Sep 8, 2024Updated 2 years ago
- InteractionDrawer is a JavaScript library for the drawing of highly interactive 2D ligand interaction diagrams.☆31Oct 16, 2023Updated 3 years ago
- ☆14Sep 1, 2026Updated last month
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 6 years ago
- Code available for the quantitative pharmacophores☆13Sep 7, 2022Updated 4 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Template-directed automatic generation of transition state structures.☆11Nov 22, 2016Updated 9 years ago
- A tool for the perception of chemical bonds via machine learning☆10Nov 15, 2025Updated 11 months ago
- Interactive single cell RNA-seq analysis webserver!☆10Mar 15, 2023Updated 3 years ago
- FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand …☆38Aug 6, 2021Updated 5 years ago
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago
- Workshop on the preparation, execution, and analysis of protein molecular dynamics simulations☆12May 7, 2025Updated last year
- Craig plot 2.0☆11Jan 29, 2020Updated 6 years ago
- Analysis of non-covalent interactions in MD trajectories☆72Jan 3, 2025Updated last year
- ☆12Aug 6, 2024Updated 2 years ago
- 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.
- scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks☆10Aug 4, 2020Updated 6 years ago
- Implementation of Protein Invariant Point Packer (PIPPack)☆37May 28, 2024Updated 2 years ago
- QM/MM interfacing in Python☆10Feb 12, 2019Updated 7 years ago
- Protein surface topographical mapping tool☆29Aug 17, 2023Updated 3 years ago
- A python interface of EPISOL, with water placement and utilities.☆11Nov 5, 2025Updated 11 months ago
- Pytorch implementation of Pocket2Drug: a generative deep learning model to predict binding drugs for ligand-binding sites.☆22May 19, 2022Updated 4 years ago
- Genetic algorithm to convert 3D-RISM solvent densities to explicit water molecules in binding pockets☆13Dec 19, 2017Updated 8 years ago