Yue Yang

发表

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap

Felice C Lightstone, Sergio E Wong, Sergio E. Wong, 2013, Expert opinion on drug discovery.

Constructing high-accuracy theoretical Raman spectra of SARS-CoV-2 spike proteins based on a large fragment method

Bo Li, Minjie Zhou, Qiang Yang, 2022, Chemical Physics Letters.

Understanding a Substrate’s Product Regioselectivity in a Family of Enzymes: A Case Study of Acetaminophen Binding in Cytochrome P450s

Sergio E. Wong, S. Wong, F. Lightstone, 2014, PloS one.

D-π-A type carbazole and triphenylamine derivatives with different π-conjugated units: Tunable aggregation-induced emission (AIE) and mechanofluorochromic properties

S. Pu, Yue Yang, Zhao Chen, 2022, Journal of Photochemistry and Photobiology A: Chemistry.

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Jonathan E. Allen, Tajana Rosing, Yue Yang, 2022, Journal of chemical theory and computation.

Development and application of ribonucleic acid therapy strategies against COVID-19

Mu-ya Liu, Yue Yang, Bifang He, 2022, International journal of biological sciences.

Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes.

K. Merz, Yue Yang, Michael N. Weaver, 2009, The journal of physical chemistry. A.

Visualizing Intramolecular Dynamics of Membrane Proteins

S. Tsuda, H. Sekiguchi, Y. Sasaki, 2022, International journal of molecular sciences.

Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase.

Kenneth M Merz, Dhruva K. Chakravorty, Yue Yang, 2010, Biochemistry.

Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS.

K. Merz, C. Fierke, B. Wang, 2012, Journal of the American Chemical Society.

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

K. Merz, L. Song, Yue Yang, 2017, Biochemistry.

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).

Kenneth M Merz, Yue Yang, K. Merz, 2010, Journal of chemical theory and computation.

Catalytic mechanism of aromatic prenylation by NphB.

K. Merz, Guanglei Cui, B. Wang, 2012, Biochemistry.

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins

Helgi I. Ingólfsson, Timothy S. Carpenter, A. Voter, 2020, Proceedings of the National Academy of Sciences.

Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

Prabhakar R. Gudla, D. Esposito, F. McCormick, 2020, eLife.

Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking

Y. Shinkai, S. Tsuda, Motomichi Doi, 2022, Biochemistry and biophysics reports.

Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline

Oscar A. Negrete, Sergio E. Wong, Edwin A. Saada, 2021, Frontiers in Molecular Biosciences.

Development of a Correlative Strategy To Discover Colorectal Tumor Tissue Derived Metabolite Biomarkers in Plasma Using Untargeted Metabolomics.

Fan Zhang, Yuanyuan Zhang, Kai Yang, 2019, Analytical chemistry.

PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel

Lusheng Wang, Yue Yang, Yizhou J. He, 2022, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.

Greg L. Hura, J. Tainer, F. Lightstone, 2018, Biochemistry.

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer

Peer-Timo Bremer, Lars Schneidenbach, Claudia Misale, 2019, SC.

Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method

Sergio E. Wong, Marisa W. Torres, Jonathan E. Allen, 2023, bioRxiv.

Origin of Product Selectivity in a Prenyl Transfer Reaction from the Same Intermediate: Exploration of Multiple FtmPT1-Catalyzed Prenyl Transfer Pathways

K. Merz, Yue Yang, L. Pan, 2014, Biochemistry.

High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models

Stewart He, Adam Zemla, Felice C. Lightstone, 2021, SC21: International Conference for High Performance Computing, Networking, Storage and Analysis.

Chiral Tetracoordinate Organoboranes Based on Double B←N Bridged Bipyridine with Circularly Polarized Luminescence

Chuandong Dou, Yue Yang, K. Ye, 2022, Materials Chemistry Frontiers.

Positive charge in the complementarity-determining regions of synthetic nanobody prevents aggregation.

Xiaorui Chen, Xiaowen He, Yue Yang, 2021, Biochemical and biophysical research communications.