32 skills found · Page 1 of 2
Superzchen / IFeatureiFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.
Profluent-AI / E1Profluent-E1 family of Protein Encoder Models
royerlab / CytoselfSelf-supervised models for encoding protein localization patterns from microscopy images
althonos / Mini3diA NumPy port of the foldseek code for encoding protein structures to 3di.
meneshail / TopoDiffCode release for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding"
DeepGraphLearning / SiamDiffCode for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)
YAndrewL / CLAPEcontrastive learning and pre-trained encoder for protein-ligand binding sites prediction
finnlueth / ProtProfileMDProtein Language Modeling beyond static folds reveals sequence-encoded flexibility
HySonLab / Ligand GenerationTarget-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning
DFrolova / MULANMULAN: Multimodal Protein Language Model for Sequence and Structure Encoding
shiningsunnyday / GeoBPEGeometric Byte Pair Encoding of Protein Structure (ICLR 2026)
JueWangTHU / CLAPE SMBContrastive learning and pre-trained encoder (CLAPE) for protein-small molecules binding (SMB) sites prediction
PNNL-CompBio / SnekmerPipeline to apply encoded Kmer analysis to protein sequences
Ruheng-W / PepBCLWe propose PepBCL, a novel BERT (Bidirectional Encoder Representation from Transformers)-based Contrastive Learning framework to predict the protein-Peptide binding residues based on protein sequences only.
BoHuangLab / CELL E 2Multimodal encoder-only transformer model for image-based protein predictions
deeprob / PssmproA python tool for numerically encoding protein sequences based on PSSM profile
RoniGurvich / PeptrieverBi-Encoder approach for large-scale protein-peptide binding search
johnbachman / FamplexNamespace encoding hierarchical relationships between proteins, protein families, and protein complexes.
argearriojas / 2dlattice ProtfoldImplementation of protein folding on 2D lattice on D-Wave QPU, using turn ancilla encoding (Babbush 2013). Conventional Monte Carlo Simulated Annealing is also included as a sepate approach
T-B-F / Aae4seqTools to encode protein sequences using an Adversarial AutoEncoder
