Pawan Neupane

Alex Morehead, Nabin Giri, Jian Liu et al.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baseline algorithms, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel binding poses; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Bhanu Prakash Vangala, Sajid Mahmud, Pawan Neupane et al.

Artificial Intelligence (AI), particularly Large Language Models (LLMs), is transforming scientific discovery, enabling rapid knowledge generation and hypothesis formulation. However, a critical challenge is hallucination, where LLMs generate factually incorrect or misleading information, compromising research integrity. To address this, we introduce HalluMatData, a benchmark dataset for evaluating hallucination detection methods, factual consistency, and response robustness in AI-generated materials science content. Alongside this, we propose HalluMatDetector, a multi-stage hallucination detection framework that integrates intrinsic verification, multi-source retrieval, contradiction graph analysis, and metric-based assessment to detect and mitigate LLM hallucinations. Our findings reveal that hallucination levels vary significantly across materials science subdomains, with high-entropy queries exhibiting greater factual inconsistencies. By utilizing HalluMatDetector verification pipeline, we reduce hallucination rates by 30% compared to standard LLM outputs. Furthermore, we introduce the Paraphrased Hallucination Consistency Score (PHCS) to quantify inconsistencies in LLM responses across semantically equivalent queries, offering deeper insights into model reliability.

Alex Morehead, Nabin Giri, Jian Liu et al.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baseline algorithms, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel binding poses; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Pawan Neupane, Jian Liu, Jianlin Cheng

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising four large-scale, labeled datasets generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16). PSBench includes over one million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods. These results highlight PSBench as a valuable resource for advancing EMA research in protein complex modeling. PSBench is publicly available at: https://github.com/BioinfoMachineLearning/PSBench.