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Nature Methods|February 8, 2022
CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networksXi Zhang, Biao Zhang, Lydia Freddolino, et al.Nucleic Acids Research|July 31, 2023
BioLiP2: an updated structure database for biologically relevant ligand-protein interactionsChengxin Zhang, Xi Zhang, Lydia Freddolino, et al.Nucleic Acids Research|May 5, 2017
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction informationChengxin Zhang, Lydia Freddolino, Yang ZhangNature Protocols|July 3, 2025
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-alignChengxin Zhang, Lydia Freddolino, Yang ZhangProteins|August 31, 2023
Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15Wei Zheng, Qiqige Wuyun, Lydia Freddolino, et al.Briefings in Bioinformatics|March 22, 2024
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fittingZiying Zhang, Yaxian Cai, Biao Zhang, et al.The Journal of Physical Chemistry. B|May 5, 2017
Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy LandscapesMorteza Khabiri, Lydia FreddolinoPlos Biology|July 29, 2024
FURNA: A database for functional annotations of RNA structuresChengxin Zhang, Lydia FreddolinoAnnual Review of Cell and Developmental Biology|May 8, 2012
Beyond homeostasis: a predictive-dynamic framework for understanding cellular behaviorLydia Freddolino, Saeed TavazoieBriefings in Bioinformatics|July 22, 2024
A large-scale assessment of sequence database search tools for homology-based protein function predictionChengxin Zhang, Lydia FreddolinoPageof 1,842