Jian Liu

Improving AlphaFold3 by Engineering MSA and Template Inputs

This paper improves AlphaFold3 by using customized MSAs and templates, achieving higher accuracy in structure prediction for monomers, multimers, and protein-ligand complexes.

Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16

The paper improves protein complex structure prediction by integrating AlphaFold2 and 3 with enhanced methods in MULTICOM4, achieving high TM-scores and DockQ scores in CASP16.

Accurate Prediction of Protein Complex Stoichiometry by Integrating AlphaFold3 and Template Information

The paper predicts protein complex stoichiometry by combining AlphaFold3 and template information, achieving high accuracy in CASP16.

Estimating Protein Complex Model Accuracy Using Graph Transformers and Pairwise Similarity Graphs

GATE estimates protein complex model accuracy using graph transformers on pairwise similarity graphs, achieving high correlation and low ranking loss on CASP15 and CASP16 datasets.

A Gated Graph Transformer for Protein ComplexStructure Quality Assessment and its Performancein CASP15

This paper introduces DProQA, a gated graph transformer for assessing the quality of predicted protein complex structures, achieving third place in CASP15 quality assessment.