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Search results for protein pdb
pdb
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protein
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102 search results found
Molecularnodes
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729
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Prospr
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407
ProSPr: Protein Structure Prediction
Plip
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320
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
Pdb Tools
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319
A dependency-free cross-platform swiss army knife for PDB files.
Pypdb
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258
A Python API for the RCSB Protein Data Bank (PDB)
Ribbon
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208
Ribbon diagrams of proteins in #golang.
P2rank
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193
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
Deepfri
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156
Deep functional residue identification
Deeprank
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145
This repository has been integrated in https://github.com/DeepRank/deeprank2
Icn3d
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135
web-based protein structure viewer and analysis tool interactively or in batch mode
Dssp
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113
Application to assign secondary structure to proteins
Proteinsecondarystructure Cnn
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93
Protein Secondary Structure predictor using Convolutional Neural Networks
Atomium
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92
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
Biostructures.jl
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77
A Julia package to read, write and manipulate macromolecular structures (particularly proteins)
Protein Science
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76
A collection of useful tutorials for Protein Science
Pdbtools
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68
A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files
Mitos.jl
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64
Mutual Information Tools for protein Sequence analysis in Julia
Coronavirus_structural_task_force
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60
Repository for the molecular structures related with Corona virusses and their re-processing
Vscoding Sequence
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56
VSCode Extension for interactively visualising protein structure data in the editor
Deepchem Gui
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53
A simple web GUI for DeepChem
Dove
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52
A Deep-learning based dOcking decoy eValuation mEthod
Cath Tools
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51
Protein structure comparison tools such as SSAP and SNAP
Jolecule
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48
Javascript viewer for proteins and DNA with animated views
Proteingcn
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47
ProteinGCN: Protein model quality assessment using Graph Convolutional Networks
Deepdrug3d
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46
A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets.
Protocolgromacs
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40
Automatic gromacs protocol from preparation to production with ligand parametrization through
Md Ifp
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40
MD trajectory analysis using protein-ligand Interaction Fingerprints
Pylipid
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37
A python toolkit for analysing membrane protein-lipid interactions.
Localpdb
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36
Python package to manage protein structures and their annotations
Caviar
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36
// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition
Ramanet
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31
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
Pdb Benchmarks
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26
Benchmarking common tasks on proteins in various languages and packages
Onionnet
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24
A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction
Pdbcolor
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24
Python code to color a PDB structure based on parameters from a multiple sequence alignment
Deltavinaxgb
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24
This is a machine-learning based protein-ligand scoring function.
Glycosylator
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23
Framework for the rapid modeling glycans and glycoproteins.
Lemon
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22
A framework for rapidly mining structural information from the Protein Data Bank
Proteinensembles.jl
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21
Generate and perturb protein structural ensembles using the ExProSE algorithm
Lightdock Python2.7
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20
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Getpdb
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20
Download pdb/protein structures from Uniprot id; This script will download related PDB files, extract chains(Optional), remove duplicates(Optional, maybe lost some conformation changed structures) and save as "UniprotID-PDBID-ModelID-ChainID.pdb/cif".
Pgm
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19
Probabilistic Graphical Models in Python3.
Hpdb
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19
PDB parser in Haskell
Biovec
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19
ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.
Iscore
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19
iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines
Michelanglo App
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17
A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site
Emap2sec
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15
Emap2sec is a computational tool to identify protein secondary structures
Rosettadesign
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15
RosettaDesign using PyRosetta
Manuscript_ab_epitope_interaction
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14
Gcn For Structure And Function
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14
Code for reproducing results of "Unsupervised embeddings is all you need for protein function prediction"
P2rank Datasets
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14
Datasets for P2Rank project. https://github.com/rdk/p2rank
Dockingml
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14
A package for MD, Docking and Machine learning drug discovery pipeline
Emacs Pdb Mode
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12
pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.
Dips
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12
Database of Interacting Protein Structures (DIPS)
Deepalign
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12
DeepAlign: the protein structure analysis toolkit
Pdb_eda
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12
A Python tool for parsing and analyzing electron density maps data available from the worldwide Protein Data Bank
Prankwebapp
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11
Web application for protein-ligand binding sites analysis and visualization
Popscomp
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11
Solvent Accessible Surface Areas of Biomolecules and their Complexes
Enlighten2
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11
Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems
Imvs
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11
A simple protein molecular visualisation app implementing with Apple Swift for iOS. Provides balls and balls & sticks display mode in CPK colours.
Allopred
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11
Predict allosteric pockets on proteins
Waterdock 2.0
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10
WaterDock-2.0 implementation with Akshay Sridhar
Mode Task
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10
PCA and normal mode analysis of proteins
Pose
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10
A bare metal Python library for building and manipulating protein molecular structures
Mgpfusion
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10
mGPfusion is a Gaussian process based method for predicting stability changes upon single and multiple mutations of proteins that complements the available experimental data with large amounts of simulated data.
Kripo
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10
Command line tool to generate Kripo fingerprints from Protein Data Bank files.
Proteinfeatureview
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9
The Protein Feature View - a SVG library for visualising protein annotations
Fragalysis Api
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9
A python API for fragalysis (fragalysis.diamond.ac.uk)
Pssmgen
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9
Generates consistent PSSM and/or PDB files for protein-protein complexes
Py_protein_utils
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9
Python utilities for handling Rosetta output and PDB files
Bm5 Clean
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9
Docking benchmark 5 - cleaned and ready to use for HADDOCK
Deepfold
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9
Learning structural motif representations for efficient protein structure search
Protcad
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8
Patoz
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8
Protein Data Bank (pdb) file parser
Strucmotif Search
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8
Real-time structure motif searching in protein 3D structures using an inverted index strategy
Ponder
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8
PointNet for Deep Rank: protein-protein interaction scoring using neural networks
Prodigy Lig
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8
Prediction of Protein-Small molecule binding affinities
Protein_seq_des
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8
Code for our paper "Protein sequence design with a learned potential"
Struct2graph
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8
A PyTorch implementation of GCN with mutual attention for protein-protein interaction prediction
Capnetprotstruct
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7
Capsule Networks for improving protein secondary structure prediction accuracy
Bipspi
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7
Partner specific prediction of protein binding sites
Aposteriori
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7
DNN based protein design.
Moltimate Backend
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7
A protein active site alignment tool
G2s
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7
A standalone component to provide mappings between protein sequence positions and PDB 3D protein structure models
Rcsb Saguaro App
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7
RCSB Saguaro 1D Feature Viewer Web App
Consurf
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7
Evolutionary conservation estimation of residues or nucleotides
Bindkin
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6
A structural benchmark to measure point mutations’ impact on kinase-ligand interactions
Protestar
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6
Protein Structure Archiver
Structureanalyzer
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6
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
Pywater
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6
Biodownloader
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6
📦 A Command Line Tool for downloading protein structures, sequences and MSAs
Predictive Protein Classification Naive Bayes Classifier
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6
Orgpymolpysnips
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6
Antibody Mutations
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6
Assessing the impact of mutations on antibody-antigen binding affinity
Kripodb
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6
Library to interact with Kripo fragment, fingerprint and similarity data files.
2d Protein Shape Matching
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6
find 2d views of proteins that look like your favorite shape
Denovoprediction
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5
De Novo Protein Tertiary Structure Prediction Pipeline
Intpred
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5
Biographs
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5
Python class to easily deal with protein networks.
Pdbtools
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5
Collection of modules for PDB file parsing, linear algebra calculations and structure modify.
Ppiprediction
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5
software used in the paper "Exploring the potential of 3D Zernike descriptors and SVM for protein–protein interface prediction"
Related Searches
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Interaction Protein (204)
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