Ruhong Zhou

26 papers A 1B 1Misc 4Journal 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
Decoding TCR recognition via geometric deep learning of immunological fingerprints.
Briefings Bioinform.
Chun Shang, Kevin C. Chan, Ruhong Zhou
2025 J jnl
A free energy perturbation-assisted machine learning strategy for mimotope screening in neoantigen-based vaccine design.
Briefings Bioinform.
Qinglu Zhong, Kevin C. Chan, Lei Fu, Ruhong Zhou
2025 J jnl
Integrating Physics-Based Simulations with Data-Driven Deep Learning Represents a Robust Strategy for Developing Inhibitors Targeting the Main Protease.
J. Chem. Inf. Model.
Yanqing Yang, Yangwei Jiang, Dong Zhang, Leili Zhang, Ruhong Zhou
2024 J jnl
IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.
PLoS Comput. Biol.
Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang, Ruhong Zhou
2023 J jnl
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow.
Briefings Bioinform.
Gang Xu, Zhenwei Luo, Ruhong Zhou, Qinghua Wang, Jianpeng Ma
2021 J jnl
CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method.
BMC Bioinform.
Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong
2020 J jnl
CASTELO: Clustered Atom Subtypes aidEd Lead Optimization - a combined machine learning and molecular modeling method.
CoRR
Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong
2012 J jnl
Multiscale modeling of macromolecular biosystems.
Briefings Bioinform.
Samuel Flores, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang
2011 J jnl
Modeling mutations of influenza virus with IBM Blue Gene.
IBM J. Res. Dev.
Zhen Xia, Payel Das, Tien Huynh, Ajay K. Royyuru, Ruhong Zhou
2011 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Julie Bernauer, Samuel Flores, Xuhui Huang, Seokmin Shin, Ruhong Zhou
2010 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin
2009 J jnl
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.
J. Comput. Chem.
Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou
2009 J jnl
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.
Bioinform.
Zhen Xia, Gulei Jin, Jun Zhu, Ruhong Zhou
2008 J jnl
Massively parallel molecular dynamics simulations of lysozyme unfolding.
IBM J. Res. Dev.
Ruhong Zhou, Maria Eleftheriou, Chung-Chau Hon, Robert S. Germain, Ajay K. Royyuru, Bruce J. Berne
2007 J jnl
PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.
Bioinform.
Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur
2006 Misc conf
Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L.
International Conference on Computational Science (2)
Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, T. J. Christopher Ward, Mark Giampapa, Yuriy Zhestkov, Michael Pitman, Frank Suits, Alan Grossfield, Jed W. Pitera, William C. Swope, Ruhong Zhou, Scott Feller, Robert S. Germain
2006 J jnl
Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins.
Int. J. Bioinform. Res. Appl.
Ruhong Zhou, Ajay K. Royyuru, Prasanna Athma, Frank Suits, B. David Silverman
2006 A conf
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L.
IPDPS
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. Pitera, Blake G. Fitch, Ruhong Zhou, Robert S. Germain
2005 J jnl
A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage.
J. Bioinform. Comput. Biol.
Lei Ye, Huajun Chen, Ting Liu, Zhaohui Wu, Jingyuan Li, Ruhong Zhou
2005 J jnl
Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a
PLoS Comput. Biol.
Laxmi Parida, Ruhong Zhou
2005 B conf
Protein folding trajectory analysis using patterned clusters.
APBC
J. Feng, Laxmi Parida, Ruhong Zhou
2003 J jnl
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations.
J. Comput. Chem.
George A. Kaminski, Richard A. Friesner, Ruhong Zhou
2003 J jnl
Blue Matter, an application framework for molecular simulation on Blue Gene.
J. Parallel Distributed Comput.
Blake G. Fitch, Robert S. Germain, Mark P. Mendell, Jed W. Pitera, Michael Pitman, Aleksandr Rayshubskiy, Yuk Yin Sham, Frank Suits, William C. Swope, T. J. Christopher Ward, Yuriy Zhestkov, Ruhong Zhou
2002 Misc conf
Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling.
Pacific Symposium on Biocomputing
Ruhong Zhou, B. David Silverman
2002 J jnl
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests.
J. Comput. Chem.
George A. Kaminski, Harry A. Stern, Bruce J. Berne, Richard A. Friesner, Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou, Thomas A. Halgren
2001 J jnl
Blue Gene: A vision for protein science using a petaflop supercomputer.
IBM Syst. J.
Frances E. Allen, George S. Almási, Wanda Andreoni, Daniel K. Beece, Bruce J. Berne, Arthur A. Bright, José R. Brunheroto, Calin Cascaval, José G. Castaños, Paul Coteus, Paul Crumley, Alessandro Curioni, Monty Denneau, Wilm E. Donath, Maria Eleftheriou, Blake G. Fitch, Bruce M. Fleischer, Christos J. Georgiou, Robert S. Germain, Mark Giampapa, Donna L. Gresh, Manish Gupta, Ruud A. Haring, C. T. Howard Ho, Peter H. Hochschild, Susan Flynn Hummel, Tiziana Jonas, Derek Lieber, Glenn J. Martyna, Kiran K. Maturu, José E. Moreira, Dennis M. Newns, Matthew Newton, Robert Philhower, Thomas Picunko, Jed W. Pitera, Michael Pitman, Rick A. Rand, Ajay K. Royyuru, Valentina Salapura, Alda Sanomiya, Rahul S. Shah, Yuk Yin Sham, Sarabjeet Singh, Marc Snir, Frank Suits, Richard A. Swetz, William C. Swope, Nagesh K. Vishnumurthy, T. J. Christopher Ward, Henry S. Warren Jr., Ruhong Zhou