SOTAVerified

Protein Design

Formally, given the design requirements of users, models are required to generate protein amino acid sequences that align with those requirements.

Papers

Recently AddedMost HypedMost ActiveNeeds VerificationMost Verified

Showing 101–150 of 175 papers

TitleStatusHype
Generative artificial intelligence for de novo protein design—0
Score-Based Generative Models for Designing Binding Peptide BackbonesCode1
DockGame: Cooperative Games for Multimeric Rigid Protein Docking—0
Fast protein backbone generation with SE(3) flow matchingCode2
Expected flow networks in stochastic environments and two-player zero-sum gamesCode0
Backdiff: a diffusion model for generalized transferable protein backmapping—0
Boosting AND/OR-Based Computational Protein Design: Dynamic Heuristics and Generalizable UFO—0
OpenProteinSet: Training data for structural biology at scaleCode4
Hypergraph Isomorphism ComputationCode2
Metropolis Sampling for Constrained Diffusion Models—0
Practical and Asymptotically Exact Conditional Sampling in Diffusion ModelsCode1
Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language ModelsCode2
Gradient-Informed Quality Diversity for the Illumination of Discrete Spaces—0
Protein Design with Guided Discrete DiffusionCode1
Improving few-shot learning-based protein engineering with evolutionary samplingCode1
Robust Model-Based Optimization for Challenging Fitness LandscapesCode0
Knowledge-Design: Pushing the Limit of Protein Design via Knowledge RefinementCode2
Scalable Coupling of Deep Learning with Logical ReasoningCode0
Diffusion Models for Constrained DomainsCode1
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion ModelsCode2
CCPL: Cross-modal Contrastive Protein Learning—0
Protein Sequence Design with Batch Bayesian OptimisationCode0
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action—0
A Text-guided Protein Design FrameworkCode2
Geometry-Complete Diffusion for 3D Molecule Generation and OptimizationCode2
Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue CloudsCode1
RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA DesignCode1
Protein Structure Prediction until CASP15—0
AlphaFold Distillation for Protein DesignCode1
PiFold: Toward effective and efficient protein inverse foldingCode1
Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure PredictionCode0
ProGen2: Exploring the Boundaries of Protein Language ModelsCode2
Robust deep learning based protein sequence design using ProteinMPNNCode3
RITA: a Study on Scaling Up Generative Protein Sequence ModelsCode2
TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs—0
Generative De Novo Protein Design with Global ContextCode1
Generative power of a protein language model trained on multiple sequence alignmentsCode1
AlphaDesign: A graph protein design method and benchmark on AlphaFoldDBCode1
Gate-based Quantum Computing for Protein DesignCode0
Controllable Protein Design with Language Models—0
Benchmarking deep generative models for diverse antibody sequence design—0
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-designCode1
Fast fixed-backbone protein sequence and rotamer design—0
Design in the Dark: Learning Deep Generative Models for De Novo Protein Design—0
PDBench: Evaluating Computational Methods for Protein Sequence Design—0
Deep Generative Modeling for Protein Design—0
Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein DesignCode1
ProDCoNN-server: a web server for protein sequence prediction and design from a three-dimensional structureCode0
Efficient generative modeling of protein sequences using simple autoregressive models—0
Mimetic Neural Networks: A unified framework for Protein Design and Folding—0
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All datasetsCATH 4.2CATH 4.3

Benchmark Results

#ModelMetricClaimedVerifiedStatus
1GraphTransPerplexity6.63—Unverified
2StructGNNPerplexity6.4—Unverified
3AlphaDesignPerplexity6.3—Unverified
4GCAPerplexity6.05—Unverified
5GVPPerplexity5.36—Unverified
6ProteinMPNNPerplexity4.61—Unverified
7PiFoldPerplexity4.55—Unverified
8Knowledge-DesignPerplexity3.46—Unverified
#ModelMetricClaimedVerifiedStatus
1ESM-IFPerplexity6.44—Unverified
2GVP-largePerplexity6.17—Unverified