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Hui Lu

Research Profile

Concepts & Ideas

Physiology

Protein Folding

Activities & Behaviors

Chemicals & Drugs

Procedures

Phenomena

Disorders

Protein Denaturation

Occupations

Computational Biology

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Publications

TOP 3
Georgi Z Genchev; Tomoyoshi Kobayashi; Hui Lu
Calcium induced regulation of skeletal troponin - computational insights from molecular dynamics simulations.
Morten Källberg; Robert Langlois; Nitin Bhardwaj; Hui Lu
A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.
Morten Källberg; Hui Lu; Jian Peng; Haipeng Wang; Sheng Wang; Zhiyong Wang; Jinbo Xu
Template-based protein structure modeling using the RaptorX web server.

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All Publications

2013: Georgi Z Genchev; Tomoyoshi Kobayashi; Hui Lu
Calcium induced regulation of skeletal troponin - computational insights from molecular dynamics simulations.
PloS one 2013;8(3):e58313.
2012: Morten Källberg; Robert Langlois; Nitin Bhardwaj; Hui Lu
A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.
Bioinformatics (Oxford, England) 2012;28(18):i431-i437.
2012: Morten Källberg; Hui Lu; Jian Peng; Haipeng Wang; Sheng Wang; Zhiyong Wang; Jinbo Xu
Template-based protein structure modeling using the RaptorX web server.
Nature protocols 2012;7(8):1511-22.
2012: Chengzhi He; Georgi Z Genchev; Hui Lu; Hongbin Li
Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations.
Journal of the American Chemical Society 2012;134(25):10428-35.
2012: Yong Chen; Nitin Bhardwaj; Randy A Hall; Barry Honig; Morten Källberg; Svetlana Kurilova; Hui Lu; Ren Sheng; Antonina Silkov; Moe P Tun; Wonhwa Cho
Genome-wide functional annotation of dual-specificity protein- and lipid-binding modules that regulate protein interactions.
Molecular cell 2012;46(2):226-37.
2012: Ren Sheng; Ewa Stec; Moe P Tun; Heon Yung Gee; Nichole R Blatner; Yong Chen; Takahiro K Fujiwara; Min Goo Lee; Ji Hye Hong; Morten Källberg; Yonjung Kim; Akihiro Kusumi; Hui Lu; Heather R Melowic; Kwang Pyo Kim; Wonhwa Cho
Cholesterol modulates cell signaling and protein networking by specifically interacting with PDZ domain-containing scaffold proteins.
Nature communications 2012;3():1249.
2011: Rima Chaudhuri; Hui Lu; Sishi Tang; Guijun Zhao; David A Case; Michael E Johnson
Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications.
Journal of molecular biology 2011;414(2):272-88.
2011: Ognjen Perišić; Hui Lu
Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols.
Physical review. E, Statistical, nonlinear, and soft matter physics 2011;84(5 Pt 2):056705.
2011: Lorna Dougan; Georgi Z Genchev; Hui Lu; Julio M Fernandez
Probing osmolyte participation in the unfolding transition state of a protein.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(24):9759-64.
2010: Matthew B Carson; Robert Langlois; Hui Lu
NAPS: a residue-level nucleic acid-binding prediction server.
Nucleic acids research 2010;38(Web Server issue):W431-5.
2010: Tzu-Ling Kuo; Sergi Garcia-Manyes; Jingyuan Li; Itay Barel; Hui Lu; Bruce J Berne; Michael Urbakh; Joseph Klafter; Julio M Fernández
Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(25):11336-40.
2010: Robert E Langlois; Hui Lu
Boosting the prediction and understanding of DNA-binding domains from sequence.
Nucleic acids research 2010;38(10):3149-58.
2010: Nitin Bhardwaj; Matthew B Carson; Alexej Abyzov; Koon-Kiu Yan; Hui Lu; Mark B Gerstein
Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.
PLoS computational biology 2010;6(5):e1000755.
2010: Morten Källberg; Hui Lu
An improved machine learning protocol for the identification of correct Sequest search results.
BMC bioinformatics 2010;11():591.
2010: Nitin Bhardwaj; Mark Gerstein; Hui Lu
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.
BMC bioinformatics 2010;11 Suppl 1():S6.
2010: Youngdae Yoon; Jiansong Tong; Park Joo Lee; Alexandra Albanese; Nitin Bhardwaj; Morten Källberg; Michelle A Digman; Hui Lu; Enrico Gratton; Yeon-Kyun Shin; Wonhwa Cho
Molecular basis of the potent membrane-remodeling activity of the epsin 1 N-terminal homology domain.
The Journal of biological chemistry 2010;285(1):531-40.
2009: Kris Meerschaert; Moe Phyu Tun; Eline Remue; Ariane De Ganck; Ciska Boucherie; Berlinda Vanloo; Gisèle Degeest; Joël Vandekerckhove; Pascale Zimmermann; Nitin Bhardwaj; Hui Lu; Wonhwa Cho; Jan Gettemans
The PDZ2 domain of zonula occludens-1 and -2 is a phosphoinositide binding domain.
Cellular and molecular life sciences : CMLS 2009;66(24):3951-66.
2009: Nitin Bhardwaj; Hui Lu
Co-expression among constituents of a motif in the protein-protein interaction network.
Journal of bioinformatics and computational biology 2009;7(1):1-17.
2009: Jing Wen; Xishu Wang; Warren Kibbe; Simon Lin; Hui Lu
Visual annotation of the gene database.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2009;2009():4175-7.
2009: Morten Källberg; Hui Lu
Structural feature extraction protocol for classifying reversible membrane binding protein domains.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2009;2009():6735-8.
2009: Georgi Z Genchev; Morten Källberg; Gamze Gürsoy; Anuradha Mittal; Lalit Dubey; Ognjen Perisic; Gang Feng; Robert Langlois; Hui Lu
Mechanical signaling on the single protein level studied using steered molecular dynamics.
Cell biochemistry and biophysics 2009;55(3):141-52.
2008: Lorna Dougan; Ainavarapu Sri Rama Koti; Georgi Genchev; Hui Lu; Julio M Fernandez
A single-molecule perspective on the role of solvent hydrogen bonds in protein folding and chemical reactions.
Chemphyschem : a European journal of chemical physics and physical chemistry 2008;9(18):2836-47.
2008: Deepak Sharma; Gang Feng; Dingyue Khor; Georgi Z Genchev; Hui Lu; Hongbin Li
Stabilization provided by neighboring strands is critical for the mechanical stability of proteins.
Biophysical journal 2008;95(8):3935-42.
2008: Debasis Manna; Nitin Bhardwaj; Mohsin S Vora; Robert V Stahelin; Hui Lu; Wonhwa Cho
Differential roles of phosphatidylserine, PtdIns(4,5)P2, and PtdIns(3,4,5)P3 in plasma membrane targeting of C2 domains. Molecular dynamics simulation, membrane binding, and cell translocation studies of the PKCalpha C2 domain.
The Journal of biological chemistry 2008;283(38):26047-58.
2008: Lorna Dougan; Gang Feng; Hui Lu; Julio M Fernandez
Solvent molecules bridge the mechanical unfolding transition state of a protein.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(9):3185-90.
2008: Robert E Langlois; Hui Lu
Intelligible machine learning with malibu.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2008;2008():3795-8.
2008: Matthew B Carson; Robert Langlois; Hui Lu
Mining knowledge for the methylation status of CpG islands using alternating decision trees.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2008;2008():3787-90.
2007: Nitin Bhardwaj; Robert V Stahelin; Guijun Zhao; Wonhwa Cho; Hui Lu
MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins.
Bioinformatics (Oxford, England) 2007;23(22):3110-2.
2007: Zhi-Qiang Ye; Shu-Qi Zhao; Ge Gao; Xiao-Qiao Liu; Robert E Langlois; Hui Lu; Liping Wei
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).
Bioinformatics (Oxford, England) 2007;23(12):1444-50.
2007: Robert E Langlois; Matthew B Carson; Nitin Bhardwaj; Hui Lu
Learning to translate sequence and structure to function: identifying DNA binding and membrane binding proteins.
Annals of biomedical engineering 2007;35(6):1043-52.
2007: Deepak Sharma; Ognjen Perisic; Qing Peng; Yi Cao; Canaan Lam; Hui Lu; Hongbin Li
Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(22):9278-83.
2007: Nitin Bhardwaj; Hui Lu
Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions.
FEBS letters 2007;581(5):1058-66.
2007: Guijun Zhao; Matthew B Carson; Hui Lu
Prediction of specific protein-DNA recognition by knowledge-based two-body and three-body interaction potentials.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2007;2007():5017-20.
2007: Gang Feng; Hui Lu
Computer simulation of I27 translocation through ClpY reveals a critical role of protein mechanical strength and local stability.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2007;2007():1213-6.
2007: Sri Rama Koti Ainavarapu; Jasna Brujic; Hector H Huang; Arun P Wiita; Hui Lu; Lewyn Li; Kirstin A Walther; Mariano Carrion-Vazquez; Hongbin Li; Julio M Fernandez
Contour length and refolding rate of a small protein controlled by engineered disulfide bonds.
Biophysical journal 2007;92(1):225-33.
2006: Nitin Bhardwaj; Robert V Stahelin; Robert E Langlois; Wonhwa Cho; Hui Lu
Structural bioinformatics prediction of membrane-binding proteins.
Journal of molecular biology 2006;359(2):486-95.
2005: Nitin Bhardwaj; Hui Lu
Correlation between gene expression profiles and protein-protein interactions within and across genomes.
Bioinformatics (Oxford, England) 2005;21(11):2730-8.
2005: Nitin Bhardwaj; Robert Langlois; Guijun Zhao; Hui Lu
Structure Based Prediction of Binding Residues on DNA-binding Proteins.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2005;3():2611-4.
2005: Guijun Zhao; Hui Lu
Development of a Grid-based statistical potential for protein structure prediction.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2005;6():6064-7.
2005: Nitin Bhardwaj; Robert E Langlois; Guijun Zhao; Hui Lu
Kernel-based machine learning protocol for predicting DNA-binding proteins.
Nucleic acids research 2005;33(20):6486-93.
2004: Nishant Bhasin; Philippe Carl; Sandy Harper; Gang Feng; Hui Lu; David W Speicher; Dennis E Discher
Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding.
The Journal of biological chemistry 2004;279(44):45865-74.
2004: Robert E Langlois; Alice Diec; Yang Dai; Hui Lu
Kernel based approach for protein fold prediction from sequence.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2004;4():2885-8.
2003: Hui Lu; Jeffrey Skolnick
Application of statistical potentials to protein structure refinement from low resolution ab initio models.
Biopolymers 2003;70(4):575-84.
2003: Mariano Carrion-Vazquez; Hongbin Li; Hui Lu; Piotr E Marszalek; Andres Oberhauser; Julio M Fernandez
The mechanical stability of ubiquitin is linkage dependent.
Nature structural biology 2003;10(9):738-43.
2003: Long Lu; Adrian Arakaki; Hui Lu; Jeffrey Skolnick
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.
Genome research 2003;13(6A):1146-54.
2003: Hui Lu; Long Lu; Jeffrey Skolnick
Development of unified statistical potentials describing protein-protein interactions.
Biophysical journal 2003;84(3):1895-901.
2002: Long Lu; Hui Lu; Jeffrey Skolnick
MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
Proteins 2002;49(3):350-64.
2002: Hongbin Li; Wolfgang A Linke; Andres Oberhauser; Mariano Carrion-Vazquez; Jason G Kerkvliet; Hui Lu; Piotr E Marszalek; Julio M Fernandez
Reverse engineering of the giant muscle protein titin.
Nature 2002;418(6901):998-1002.
2002: Daisuke Kihara; Yang Zhang; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(9):5993-8.
2002: Mu Gao; Hui Lu; Klaus Schulten
Unfolding of titin domains studied by molecular dynamics simulations.
Journal of muscle research and cell motility 2002;23(5-6):513-21.
2001: Daisuke Kihara; Hui Lu; Andrzej Kolinski; Jeffrey Skolnick
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(18):10125-30.
2001: Hui Lu; Jeffrey Skolnick
A distance-dependent atomic knowledge-based potential for improved protein structure selection.
Proteins 2001;44(3):223-32.
1999: Piotr E Marszalek; Hui Lu; Hongbin Li; Mariano Carrion-Vazquez; Andres Oberhauser; K Schulten; Julio M Fernandez
Mechanical unfolding intermediates in titin modules.
Nature 1999;402(6757):100-3.
1999: Hui Lu; Klaus Schulten
Steered molecular dynamics simulations of force-induced protein domain unfolding.
Proteins 1999;35(4):453-63.
1999: André Krammer; Hui Lu; B Isralewitz; Klaus Schulten; Viola Vogel
Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch.
Proceedings of the National Academy of Sciences of the United States of America 1999;96(4):1351-6.