Ruhong Zhou

According to our database, Ruhong Zhou authored at least 21 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation.

Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang, Ruhong Zhou

PLoS Comput. Biol., 2024

2023

OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow.

Gang Xu, Zhenwei Luo, Ruhong Zhou, Qinghua Wang, Jianpeng Ma

Briefings Bioinform., September, 2023

2021

CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method.

Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong

BMC Bioinform., 2021

2012

Multiscale modeling of macromolecular biosystems.

Samuel Flores, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang

Briefings Bioinform., 2012

2011

Modeling mutations of influenza virus with IBM Blue Gene.

Zhen Xia, Payel Das, Tien Huynh, Ajay K. Royyuru, Ruhong Zhou

IBM J. Res. Dev., 2011

2010

Session Introduction.

Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.

Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou

J. Comput. Chem., 2009

Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.

Zhen Xia, Gulei Jin, Jun Zhu, Ruhong Zhou

Bioinform., 2009

2008

Massively parallel molecular dynamics simulations of lysozyme unfolding.

Ruhong Zhou, Maria Eleftheriou, Chung-Chau Hon, Robert S. Germain, Ajay K. Royyuru, Bruce J. Berne

IBM J. Res. Dev., 2008

2007

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory.

Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur

Bioinform., 2007

2006

Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins.

Ruhong Zhou, Ajay K. Royyuru, Prasanna Athma, Frank Suits, B. David Silverman

Int. J. Bioinform. Res. Appl., 2006

Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L.

Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. Pitera, Blake G. Fitch, Ruhong Zhou, Robert S. Germain

Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L.

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

Proceedings of the Computational Science, 2006

2005

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a <i>β</i>-Hairpin.

Laxmi Parida, Ruhong Zhou

PLoS Comput. Biol., 2005

A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage.

Lei Ye, Huajun Chen, Ting Liu, Zhaohui Wu, Jingyuan Li, Ruhong Zhou

J. Bioinform. Comput. Biol., 2005

Protein folding trajectory analysis using patterned clusters.

J. Feng, Laxmi Parida, Ruhong Zhou

Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

2003

Blue Matter, an application framework for molecular simulation on Blue Gene.

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

J. Parallel Distributed Comput., 2003

A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations.

George A. Kaminski, Richard A. Friesner, Ruhong Zhou

J. Comput. Chem., 2003

2002

Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests.

George A. Kaminski, Harry A. Stern, Bruce J. Berne, Richard A. Friesner, Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou, Thomas A. Halgren

J. Comput. Chem., 2002

Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling.

Ruhong Zhou, B. David Silverman

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001

Blue Gene: A vision for protein science using a petaflop supercomputer.

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

IBM Syst. J., 2001