gistfile1.txt

LatentDE  Latent-based Directed Evolution accelerated by Gradient Ascent for Protein Sequence Design
Assessing interaction recovery of predicted protein-ligand poses
Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data
Improving Antibody Design with Force-Guided Sampling in Diffusion Models
Equivariant Blurring Diffusion for Multiscale Generation of Molecular Conformer
Active Learning for Affinity Prediction of Antibodies
IgBlend  Unifying 3D Structure and Sequence for Antibody LLMs
Learning the Language of Protein Structures
moPPIt  De Novo Generation of Motif-Specific Binders with Protein Language Models
Improving generalisability of 3D binding affinity models in low data regimes
Active Learning for Energy-Based Antibody Optimization and Enhanced Screening
Conditional Enzyme Generation Using Protein Language Models with Adapters
Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules
Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models
SPECTRE  A Spectral Transformer for Molecule Identification
FlowPacker  protein side-chain packing with torsional flow matching
Similarity-Quantized Relative Difference Learning for Improved Molecular Activity Prediction
HERMES  Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction
Adapting protein language models for structure-conditioned design
Allo-Allo  Data-efficient prediction of allosteric sites
CryoSPIN  Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
GFlowNet Pretraining with Inexpensive Rewards
Benchmarking text-integrated protein language model embeddings and embedding fusion on diverse downstream tasks
RNAgrail  graph neural network and diffusion model for RNA 3D structure prediction
The OMG dataset  An Open MetaGenomic corpus for mixed-modality genomic language modeling
Functional Alignment of Protein Language Models via Reinforcement Learning with Experimental Feedback
Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models
EpiGraph  Recommender-Style Graph Neural Networks for Highly Accurate Prediction of Conformational B-Cell Epitopes
MF-LAL  Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning
Higher-Order Message Passing for Glycan Representation Learning
LOCAS  Multi-label mRNA Localization with Supervised Contrastive Learning
Does Structural Information Improve ESM3 for Protein Binding Affinity Prediction 
Unified Sampling and Ranking for Protein Docking with DFMDock
Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments
Protein Sequence Domain Annotation using Language Models
ProtComposer  Compositional Protein Structure Generation with 3D Ellipsoids
Rapid protein structure assessment via a forward model for NMR spectra
PropEn  Optimizing Proteins with Implicit Guidance
Bayesian Optimisation for Protein Sequence Design  Gaussian Processes with Zero-Shot Protein Language Model Prior Mean
Bio-xLSTM  Generative modeling  representation and in-context learning of biological and chemical sequences
Retrieval Augmented Protein Language Models for Protein Structure Prediction
CompassDock  A Comprehensive Accurate Assessment Approach for Deep Learning-Based Molecular Docking in Inference and Fine-Tuning
BoostMD  Accelerating Molecular Sampling using ML Force Field Feature
DockFormer  Efficient Multi-Modal Receptor-Ligand Interaction Prediction using Pair Transformer
Cryo-EM images are intrinsically low dimensional
Open-source Tools for CryoET Particle Picking Machine Learning Competitions
Protein Language Model Fitness is a Matter of Preference
Balancing Locality and Reconstruction in Protein Structure Tokenizer
What has AlphaFold3 learned about antibody and nanobody docking and what remains unsolved
HelixFlow  SE 3  equivariant Full-atom Design of Peptides With Flow-matching Models
MolMix  A Simple Yet Effective Baseline for Multimodal Molecular Representation Learning
Integrating Macromolecular X-ray Diffraction Data with Variational Inference
Fine-Tuning Discrete Diffusion Models via Reward Optimization  Applications to DNA and Protein Design
Low-N OpenFold fine-tuning improves peptide design without additional structures
SPRINT Enables Interpretable and Ultra-Fast Virtual Screening against Thousands of Proteomes
Ranking protein-peptide binding affinities with protein language models
Generating and scoring stable proteins using joint structure and sequence modeling
FusOn-pLM  A Fusion Oncoprotein-Specific Language Model  via Adjusted Rate Masking
Systems-Structure-Based Drug Design
Learning the language of protein-protein interactions with ESM-Multimer
Guided Multi-objective Generative AI for Structure-based Drug Design
Tradeoffs of alignment-based and protein language models for predicting viral mutation effects
IgFlow  Flow Matching for De Novo Antibody Design
Generating and evaluating diverse sequences for protein backbones
SuperMetal  A Generative AI Framework for Rapid and Precise Metal Ion Location Prediction in Proteins
Antibody DomainBed  Out-of-Distribution Generalization in Therapeutic Protein Design
Controllable All-Atom Generation of Protein Sequence and Structure from Sequence-Only Inputs
Loop-Diffusion  an equivariant diffusion model for designing and scoring protein loops
ProteinZen  combining latent and SE 3  flow matching for all-atom protein generation
Exploring Categorical Flow Matching for 3D De Novo Molecule Generation
SynFlowNet  Design of Diverse and Novel Molecules with Synthesis Constraints
RNA-DCGen  Dual Constrained RNA Sequence Generation with LLM-Attack
RNA-GPT  Multimodal Generative System for RNA Sequence Understanding
TomoPicker  Annotation Efficient Particle Picking
AptaBLE  Aptamer Prediction
Capturing Protein Dynamics  Encoding Temporal and Spatial Dynamics from Molecular Dynamics Simulations
ProPicker  Promptable Segmentation for Particle Picking in Cryogenic Electron Tomography
Estimating protein flexibility via uncertainty quantification of structure prediction models
Generative modeling of protein ensembles guided by crystallographic electron densities
Energy-Based Flow Matching for Molecular Docking
Controlling multi-state conformational equilibria of dynamic proteins with Frame2seq