3. Biomolecular Property Prediction and Analysis Tools

DDAffinity: A neural network for predicting changes in binding affinity upon multiple mutations.
Published: June 28, 2024
Paper | Code (GitHub)

CarbonDesign: A protein sequence design method that adapts the success ingredients of AF2. CarbonDesign utilizes Inverseformer, a network architecture adapted from AlphaFold’s Evoformer. Based on scTM score, sequence recovery rate, and BLOSUM score, CarbonDesign outperformed other published methods, including versions of ProteinMPNN and ESM-IF, on CAMEO and CASP15 test sets, as well as RFdiffusion-generated backbones. CarbonDesign is also capable of predicting the effects of mutations on protein function.
Published: May 23, 2024
Paper | Preprint | Code (GitHub) | Code (Code Ocean)

PreMode: A method for gene-specific mode-of-action prediction for missense variants.
Posted: March 17, 2024
Preprint | Code (GitHub)

Evo: A long-context foundation model that generalizes across the central dogma of biology: DNA, RNA, and proteins. Evo is a 7 billion parameter model trained to generate DNA sequences and is capable of prediction and generative tasks, from molecules to whole genomes.
Posted: March 06, 2024
Preprint | Code (GitHub) | Code (PyPI) | Blog | Playground | Colab Notebook

PRESCOTT: A model and webserver for predicting the effect of missense mutations, that rivals AlphaMissense. PRESCOTT is a predictor that combines ESCOTT, an epistatic and structural model of mutational effects, with allele frequencies information from the Genome Aggregation Database (gnomAD). PRESCOTT identifies protein regions most susceptible to mutations, scores individual point mutations, and categorizes mutations as benign, pathogenic, and uncertain. The PRESCOTT model was built on protein structural models, human genomic and exomic data, and huge protein sequences across species.
Posted: Feb 06, 2024
Preprint | Code (GitLab) | Webserver | Docker Image

DeepGlycanSite: A neural network for predicting carbohydrate binding sites on proteins.
Published: Jun 17, 2024
Paper | Code (GitHub)

Colabind: A cloud-based method for predicting binding sites using CG MD simulations in the presence of chemical probes.
Published: March 21, 2024
Paper | Code (GitHub) | Colab Notebook

GrASP: A method for binding site prediction in protein structures.
Posted: Feb 03, 2024
Preprint | Code (GitHub) | Colab Notebook

DiffPALM: A method for pairing interacting protein sequences based on protein language models trained on MSAs.
Published: Jun 24, 2024
Paper | Preprint | Code (GitHub) | Code (Zenodo)

PPIscreenML: A classifier that uses AF2 models to distinguish interacting protein pairs from non-interacting pairs.
Posted: March 17, 2024
Preprint | Code (GitHub)

MAGPIE: An interactive tool for visualization and analysis of interactions between a protein or ligand and its binding partners. Posted: March 04, 2024
Preprint | Code (GitHub)

Tapioca: A pipeline for de novo prediction of dynamic protein–protein interactions.
Published: Feb 15, 2024
Paper | Code (GitHub) | Webserver

AlphaCRV: An AlphaFold-based pipeline for accurate identification of binder topologies by clustering, ranking and visualization of models. Posted: Feb 08, 2024
Preprint | Code (GitHub)

ARCTIC-3D: An automated tool and webserver to mine and rationalize protein-protein interface information for a given protein. For a given protein, ARCTIC-3D retrieves existing interface information from the PDBe-graph database, and then applies hierarchical clustering on calculated similarity values of interfaces projected on the protein structure. Information generated by ARCTIC-3D can be used as input restraints to docking methods like HADDOCK, and similar to AlphaLink and ColabDock (both using experimental restraints), to drive protein complex modeling with results comparable to prediction by AF-Multimer.
Published: Jan 06, 2024
Paper | Code (GitHub) | Webserver

PypKa: A tool and webserver for physics-based and ML-assisted protein pKa estimation and biomolecular structure preparation. PypKa prepares input structures compatible with CHARMM, AMBER and GROMOS ffs. Two additional, alternative methods are provided for pKa estimation, including PypKa, pKAI and pKAI+
Published: April 15, 2024
Paper | Code (GitHub) | Webserver

DeepKa: A tool and webserver for protein pKa prediction.
Published: March 26, 2024
Paper | Code (GitHub) | Webserver