protein-cluster-conformers: used to cluster a parsed set of monomeric protein chains via a global conformational change metric based on CA distances.
MD
MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations (standalone)
SubPEx:
ML
AFsample2: a method employing random MSA column masking to reduce the influence of co-evolutionary signals to enhance the structural diversity of models generated by the AF2 neural network
AF2-Rave: AF2-Rave combines AlphaFold2 with enhanced sampling to predict a range of conformations for a given protein sequence, aiming to generate Boltzmann-ranked conformations
AF-cluster: This method predicts multiple protein conformations using sequence clustering and AlphaFold2, aiming to capture the diversity of protein structures.
AlphaFlow: AlphaFold Meets Flow Matching for Generating Protein Ensembles. (Note: There is a preprint challenging the claims in the AF-Cluster paper. You can read it here.)
Str2Str: Str2Str is a score-based framework for zero-shot protein conformation sampling, drawing inspiration from traditional methods to sample conformations guided by a neural score network trained on the PDB database.
DeepConformer: diffusion generative model for sampling protein conformation distributions from a given amino acid sequence
ICoN: Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning
Other
AlphTraj: AlphaTraj is software designed for analyzing pocket dynamics.
DANCE: DANCE is designed to process a set of input protein 3D structures provided in Crystallographic Information File (CIF) format and output protein or protein family-specific conformational collections in CIF or PDB format.
EnGens: a computational framework for generation andanalysis of representative protein conformationalensembles (online)
