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2020 – today
- 2024
[j16]Haolin Jiang, Yulian Xu, Yunguang Tong, Dong Zhang
, Ruhong Zhou:
IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation. PLoS Comput. Biol. 20(10): 1012293 (2024)- 2023
- [j15]Gang Xu, Zhenwei Luo, Ruhong Zhou, Qinghua Wang, Jianpeng Ma:
OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow. Briefings Bioinform. 24(6) (2023) - 2021
- [j14]Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong:
CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method. BMC Bioinform. 22(1): 338 (2021) - 2020
- [i1]Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong:
CASTELO: Clustered Atom Subtypes aidEd Lead Optimization - a combined machine learning and molecular modeling method. CoRR abs/2011.13788 (2020)
2010 – 2019
- 2012
- [j13]Samuel Flores, Julie Bernauer, Seokmin Shin, Ruhong Zhou, Xuhui Huang:
Multiscale modeling of macromolecular biosystems. Briefings Bioinform. 13(4): 395-405 (2012) - 2011
- [j12]Zhen Xia, Payel Das, Tien Huynh, Ajay K. Royyuru, Ruhong Zhou:
Modeling mutations of influenza virus with IBM Blue Gene. IBM J. Res. Dev. 55(5): 7 (2011) - [c6]Julie Bernauer, Samuel Flores, Xuhui Huang, Seokmin Shin, Ruhong Zhou:
Session Introduction. Pacific Symposium on Biocomputing 2011: 177-180 - 2010
- [c5]Samuel Flores, Julie Bernauer, Xuhui Huang, Ruhong Zhou, Seokmin Shin:
Session Introduction. Pacific Symposium on Biocomputing 2010: 200-204
2000 – 2009
- 2009
- [j11]Zhen Xia, Gulei Jin, Jun Zhu, Ruhong Zhou:
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus. Bioinform. 25(18): 2309-2317 (2009) - [j10]Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou:
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. J. Comput. Chem. 30(11): 1654-1663 (2009) - 2008
- [j9]Ruhong Zhou, Maria Eleftheriou, Chung-Chau Hon, Robert S. Germain, Ajay K. Royyuru, Bruce J. Berne:
Massively parallel molecular dynamics simulations of lysozyme unfolding. IBM J. Res. Dev. 52(1-2): 19-30 (2008) - 2007
- [j8]Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir P. Mudur:
PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory. Bioinform. 23(1): 99-106 (2007) - 2006
- [j7]Ruhong Zhou, Ajay K. Royyuru, Prasanna Athma, Frank Suits, B. David Silverman:
Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins. Int. J. Bioinform. Res. Appl. 2(2): 161-176 (2006) - [c4]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:
Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L. International Conference on Computational Science (2) 2006: 846-854 - [c3]Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. Pitera, Blake G. Fitch, Ruhong Zhou, Robert S. Germain:
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L. IPDPS 2006 - 2005
- [j6]Lei Ye, Huajun Chen, Ting Liu, Zhaohui Wu, Jingyuan Li, Ruhong Zhou:
A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage. J. Bioinform. Comput. Biol. 3(6): 1351-1370 (2005) - [j5]Laxmi Parida, Ruhong Zhou:
Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β-Hairpin. PLoS Comput. Biol. 1(1) (2005) - [c2]J. Feng, Laxmi Parida, Ruhong Zhou:
Protein folding trajectory analysis using patterned clusters. APBC 2005: 95-104 - 2003
- [j4]George A. Kaminski, Richard A. Friesner, Ruhong Zhou:
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. J. Comput. Chem. 24(3): 267-276 (2003) - [j3]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:
Blue Matter, an application framework for molecular simulation on Blue Gene. J. Parallel Distributed Comput. 63(7-8): 759-773 (2003) - 2002
- [j2]George A. Kaminski, Harry A. Stern, Bruce J. Berne, Richard A. Friesner, Yixiang X. Cao, Robert B. Murphy, Ruhong Zhou, Thomas A. Halgren:
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests. J. Comput. Chem. 23(16): 1515-1531 (2002) - [c1]Ruhong Zhou, B. David Silverman:
Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling. Pacific Symposium on Biocomputing 2002: 673-684 - 2001
- [j1]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:
Blue Gene: A vision for protein science using a petaflop supercomputer. IBM Syst. J. 40(2): 310-327 (2001)
Coauthor Index
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