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Search results for protein structure
protein-structure
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173 search results found
Siteinterlock
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15
A novel approach to pose selection in protein-ligand docking based on graph theory.
Bio3d
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15
A mirror of official bio3d development site at Bitbucket: https://bitbucket.org/Grantlab/bio3d. See also bio3d website: http://thegrantlab.org/bio3d
Jupyterlabpymolpysnips
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14
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
Cbh21 Protein Solubility Challenge
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13
Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.
De Stress
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13
DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.
Lightdock Rust
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13
A Rust implementation of the LightDock macromolecular docking software
Emerald
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13
EMERALD calculates safety-windows by exploring the suboptimal alignment space
Esmpair
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12
Bib'23: Improved the Heterodimer Protein Complex Prediction with Protein Language Models
Funfoldesdata
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12
Rosetta FunFolDes – a general framework for the computational design of functional proteins.
Proteinsolver
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12
Graph neural network capable of generating novel amino acid sequences that fold into proteins with predetermined topologies.
Ramachandraw
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12
Ramachandran plotting tool
Brewery
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12
State-of-the-art ab initio prediction of 1D protein structure annotations
Pmi
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12
Python Modeling Interface
Fmol
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12
A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.
Allopred
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11
Predict allosteric pockets on proteins
Korpm
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11
Predicting the effect of mutations on protein stability using a simple orientational potential.
Alphafold Peptide Receptors
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11
Identifying peptide-receptor interactions using AlphaFold-Multimer
Prankwebapp
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11
Web application for protein-ligand binding sites analysis and visualization
Pose
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10
A bare metal Python library for building and manipulating protein molecular structures
Cazy_webscraper
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10
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
Portein
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10
2D portraits of 3D protein structures
Zincbinddb
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10
The database and API backend for ZincBind - the database of zinc binding sites
Equivariant Nn Zoo
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10
A library for building equivariant neural networks and a zoo of implementations & examples.
Sword2
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10
SWift and Optimized Recognition of protein Domains
Hotmaps
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10
Detects hotspot regions for somatic mutations in 3D protein structures
Deepmetapsicov
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9
Deep ResNet-based protein contact prediction
Vaxdesign
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9
A script that computationally designs a vaccine
Easypymol
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9
Script to facilitate the making of horizontal scripts
Farseer Nmr
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9
A software suite for automatic treatment, analysis and plotting of large and multivariable datasets of bioNMR peaklists.
Pymissense
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9
PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.
Rupee
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8
RUPEE: A fast and accurate purely geometric protein structure search
Ml Ensemble Docking
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8
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning
Md Davis
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8
MD DaVis: A python package to analyze molecular dynamics trajectories of proteins
Siteinterlock
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8
A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics
Mastic
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8
Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
Patoz
⭐
8
Protein Data Bank (pdb) file parser
Singa
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8
🍃 SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.
Spada
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7
⚔️Find splicing-led, functional changes of the proteome.
Fit3d
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7
🔍 Fit3D - An application for template-based detection of small structural motifs in protein structures and macromolecular structure data.
Peppy
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7
A VR app which allows creation and manipulation of dynamic models of polypeptides. Focus is fun and learning.
Aa_subtypes
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7
Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape
Python_scripts
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7
scripts for parsing PDB, fasta, and GO
Cancer Suppressor Gene Deep Learning
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7
Cancer Suppressor Gene and Oncogene Prediction using Deep Learning (CNN)
Pdb2uniprot
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7
Convert PDB residues to their Uniprot equivalents
Ftdmp
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7
FTDMP is a software system for running docking experiments and scoring/ranking multimeric models.
Diffpack
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7
Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
Surfstamp Public
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7
3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!)
Gdock
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6
Protein-Protein Docking using Genetic Algorithm
Exmachina
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6
Sequence aligner for accurate template-based protein structure prediction
P2rank Framework
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6
The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc.
Biojava Notebooks
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6
BioJava examples in Jupyter Notebooks
Protein Edm Demo
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6
🔢🔀 Protein structure modelling using Euclidean distance matrices (EDMs)
Utgn
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6
Universal Transforming Geometric Network for protein structure prediction.
Unity Protein Visualization
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6
Protein Visualization using Unity and C# analysis on PDB Files.
Rmf
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6
The library to support reading and writing of RMF files.
Alphacutter
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6
This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.
Scipion Chem
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6
Base Scipion plugin defining objects and protocols for CHEMoinformatics
Quantum Protein Structure Prediction
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6
Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.
Aesop
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5
Modloop
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5
Web server for automated modeling of loops in protein structures
Rif
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5
Rotamer Interaction Field Python Libraries for Computational Protein Design
Rfold
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5
a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.
Cellscape
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5
Vector graphics cartoons from protein structure
Biographs
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5
Python class to easily deal with protein networks.
Deepmainmast
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5
DeepMainmast
Protein_pretrain
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5
Multimodal Pretraining for Unsupervised Protein Representation Learning
Cathsm Server
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5
Backend server for protein structure modelling pipeline (CATH/SWISS-MODEL)
Pointsite
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5
PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms
Ps4 Dataset
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5
The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.
Protpy
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5
Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.
Vizsnp St
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5
Visualizing the effect of SNPs on protein structure using iCn3D
Diffmodeler
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5
DiffModeler: a diffusion model based protein complex structure modeling tool.
Awesome Protein Design
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5
This repository contains a collection of resources and papers on Protein Design.
101-173 of 173 search results
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