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A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and…
Graph neural networks for molecular design.
AutoDock for GPUs and other accelerators
Get protein embeddings from protein sequences
Physicochemical properties, indices and descriptors for amino-acid sequences.
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
A Set of Machine Learning Classifiers For RNA Containing Complexes
FingerPrint Kit - Python-based cheminformatics package for fingerprint-related tasks
PyMOL plugin to visualize interactions detected by the fingeRNAt program
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
A comprehensive library for computational molecular biology
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction
Listing of papers about machine learning for proteins.
WebGL accelerated JavaScript molecular graphics library