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Research Output 2004 2019

  • 708 Citations
  • 16 h-Index
  • 27 Article
  • 2 Review article
  • 1 Comment/debate
  • 1 Editorial
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Article
2019
1 Citation (Scopus)

A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library

Wang, X. S., Chen, P. H. C., Hampton, J. T., Tharp, J. M., Reed, C. A., Das, S. K., Wang, D. S., Hayatshahi, H. S., Shen, Y., Liu, J. & Liu, W. R., 28 Oct 2019, In : Angewandte Chemie - International Edition. 58, 44, p. 15904-15909 6 p.

Research output: Contribution to journalArticle

Peptide Library
Cyclic Peptides
Bacteriophages
Peptides
Cysteine
1 Citation (Scopus)

Assessing the Performance of the Nonbonded Mg 2+ Models in a Two-Metal-Dependent Ribonuclease

Zuo, Z. & Liu, J., 28 Jan 2019, In : Journal of Chemical Information and Modeling. 59, 1, p. 399-408 10 p.

Research output: Contribution to journalArticle

Ribonucleases
Metals
performance
Lennard-Jones potential
Molecular dynamics

Design, synthesis, and evaluation of N-(4-(4-phenyl piperazin-1-yl)butyl)-4-(thiophen-3-yl)benzamides as selective dopamine D3 receptor ligands

Chen, P. J., Taylor, M., Griffin, S. A., Amani, A., Hayatshahi, H., Korzekwa, K., Ye, M., Mach, R. H., Liu, J., Luedtke, R. R., Gordon, J. C. & Blass, B. E., 15 Sep 2019, In : Bioorganic and Medicinal Chemistry Letters. 29, 18, p. 2690-2694 5 p.

Research output: Contribution to journalArticle

Benzamides
Dopamine D3 Receptors
Pharmacokinetics
Dopamine Receptors
Substance-Related Disorders

Probing Protein Allostery as a Residue-Specific Concept via Residue Response Maps

Hayatshahi, H. S., Ahuactzin, E., Tao, P., Wang, S. & Liu, J., 1 Jan 2019, (Accepted/In press) In : Journal of Chemical Information and Modeling.

Research output: Contribution to journalArticle

learning method
Proteins
PDS
event
neural network

Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain

Zuo, Z., Zolekar, A., Babu, K., Lin, V. J. T., Hayatshahi, H. S., Rajan, R., Wang, Y. C. & Liu, J., Jul 2019, In : eLife. 8, e46500.

Research output: Contribution to journalArticle

Open Access
Guide RNA
DNA Cleavage
Streptococcus pyogenes
Catalysis
Clustered Regularly Interspaced Short Palindromic Repeats
2018
5 Citations (Scopus)

Analogues of Arylamide Phenylpiperazine Ligands to Investigate the Factors Influencing D3 Dopamine Receptor Bitropic Binding and Receptor Subtype Selectivity

Hayatshahi, H. S., Xu, K., Griffin, S. A., Taylor, M., Mach, R. H., Liu, J. & Luedtke, R. T., 19 Dec 2018, In : ACS Chemical Neuroscience. 9, 12, p. 2972-2983 12 p.

Research output: Contribution to journalArticle

Dopamine D3 Receptors
Ligands
Dopamine D2 Receptors
Dopamine Receptors
Nitrogen
6 Citations (Scopus)

Identification of a unique Ca 2+ -binding site in rat acid-sensing ion channel 3

Zuo, Z., Smith, R. N., Chen, Z., Agharkar, A. S., Snell, H. D., Huang, R-Q., Liu, J. & Gonzales, E. B., 1 Dec 2018, In : Nature Communications. 9, 1, 2082.

Research output: Contribution to journalArticle

Acid Sensing Ion Channels
rats
Binding Sites
acids
Rats
2 Citations (Scopus)

Stress and interferon signalling-mediated apoptosis contributes to pleiotropic anticancer responses induced by targeting NGLY1

Zolekar, A., Lin, V. J. T., Mishra, N. M., Ho, Y. Y., Hayatshahi, H. S., Parab, A., Sampat, R., Liao, X., Hoffmann, P., Liu, J., Emmitte, K. A. & Wang, Y-C., 11 Dec 2018, In : British Journal of Cancer. 119, 12, p. 1538-1551 14 p.

Research output: Contribution to journalArticle

Interferons
Melanoma
Apoptosis
Neoplasms
Systems Biology
2017
3 Citations (Scopus)

Cullin neddylation may allosterically tune polyubiquitin chain length and topology

Onel, M., Sumbul, F., Liu, J., Nussinov, R. & Haliloglu, T., 1 Mar 2017, In : Biochemical Journal. 474, 5, p. 781-795 15 p.

Research output: Contribution to journalArticle

Cullin Proteins
Polyubiquitin
Chain length
Ubiquitin-Protein Ligases
Ubiquitination
8 Citations (Scopus)

Structure and Dynamics of Cas9 HNH Domain Catalytic State

Zuo, Z. & Liu, J., 1 Dec 2017, In : Scientific Reports. 7, 1, 17271.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
Genes
Immune system
Metal ions
Conformations
2016
24 Citations (Scopus)

Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations

Zuo, Z. & Liu, J., 22 Nov 2016, In : Scientific Reports. 5, 37584.

Research output: Contribution to journalArticle

Guide RNA
Molecular Dynamics Simulation
Clustered Regularly Interspaced Short Palindromic Repeats
Ions
Catalytic Domain
16 Citations (Scopus)

Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery

Kalescky, R., Zhou, H., Liu, J. & Tao, P., Apr 2016, In : PLoS Computational Biology. 12, 4, e1004893.

Research output: Contribution to journalArticle

Proteins
Protein
protein
simulation
Simulation
2015
68 Citations (Scopus)

Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution

Brewer, K. D., Bacaj, T., Cavalli, A., Camilloni, C., Swarbrick, J. D., Liu, J., Zhou, A., Zhou, P., Barlow, N., Xu, J., Seven, A. B., Prinslow, E. A., Voleti, R., Häussinger, D., Bonvin, A. M. J. J., Tomchick, D. R., Vendruscolo, M., Graham, B., Südhof, T. C. & Rizo, J., 9 Jul 2015, In : Nature Structural and Molecular Biology. 22, 7, p. 555-564 10 p.

Research output: Contribution to journalArticle

Synaptotagmin I
SNARE Proteins
Syntaxin 1
Vesicle-Associated Membrane Protein 1
Lanthanoid Series Elements
12 Citations (Scopus)

Identifying key residues for protein allostery through rigid residue scan

Kalescky, R., Liu, J. & Tao, P., 5 Mar 2015, In : Journal of Physical Chemistry A. 119, 9, p. 1689-1700 12 p.

Research output: Contribution to journalArticle

proteins
Proteins
communication
Communication
Molecular dynamics
2013
23 Citations (Scopus)

Identifying cytochrome P450 functional networks and their allosteric regulatory elements

Liu, J., Tawa, G. J. & Wallqvist, A., 3 Dec 2013, In : PLoS ONE. 8, 12, e81980.

Research output: Contribution to journalArticle

cytochrome P-450
Cytochrome P-450 Enzyme System
Thermal Diffusion
dimerization
Thermal diffusion
2012
19 Citations (Scopus)

2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes

Liu, R., Liu, J., Tawa, G. & Wallqvist, A., 25 Jun 2012, In : Journal of Chemical Information and Modeling. 52, 6, p. 1698-1712 15 p.

Research output: Contribution to journalArticle

Metabolism
Cytochrome P-450 Enzyme System
Cytochrome P-450 CYP1A2
drug
Enzymes
12 Citations (Scopus)

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

Ripoll, D. R., Khavrutskii, I. V., Chaudhury, S., Liu, J., Kuschner, R. A., Wallqvist, A. & Reifman, J., Aug 2012, In : PLoS Computational Biology. 8, 8, e1002665.

Research output: Contribution to journalArticle

drug resistance
Drug Resistance
influenza
sialidase
Influenza
2011
37 Citations (Scopus)

Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination

Liu, J. & Nussinov, R., 25 Nov 2011, In : Journal of Biological Chemistry. 286, 47, p. 40934-40942 9 p.

Research output: Contribution to journalArticle

Cullin Proteins
Ubiquitin-Protein Ligases
Ubiquitination
Substrates
Scaffolds
2010
29 Citations (Scopus)

Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases

Liu, J. & Nussinov, R., 5 Feb 2010, In : Journal of Molecular Biology. 396, 5, p. 1508-1523 16 p.

Research output: Contribution to journalArticle

Cullin Proteins
Ubiquitin-Protein Ligases
Molecular Dynamics Simulation
Carrier Proteins
Ubiquitin
21 Citations (Scopus)

Rb×1 flexible linker facilitates cullin-RING ligase function before neddylation and after deneddylation

Liu, J. & Nussinov, R., 4 Aug 2010, In : Biophysical Journal. 99, 3, p. 736-744 9 p.

Research output: Contribution to journalArticle

Cullin Proteins
Ligases
Ubiquitin-Protein Ligases
Ubiquitination
Lysine
2009
39 Citations (Scopus)

The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: Conformational control of substrate orientation

Liu, J. & Nussinov, R., 1 Oct 2009, In : PLoS Computational Biology. 5, 10, e1000527.

Research output: Contribution to journalArticle

Cullin Proteins
Ubiquitin-Protein Ligases
Ubiquitination
ubiquitin
Ubiquitin
2008
63 Citations (Scopus)
Von Hippel-Lindau Tumor Suppressor Protein
Binding Sites
von Hippel-Lindau Disease
Tumor Suppressor Proteins
Mutation
2007
47 Citations (Scopus)

Surface complexes of phthalic acid at the hematite/water interface

Hwang, Y. S., Liu, J., Lenhart, J. J. & Hadad, C. M., 1 Mar 2007, In : Journal of Colloid and Interface Science. 307, 1, p. 124-134 11 p.

Research output: Contribution to journalArticle

Hematite
Acids
Water
Adsorption
Ionic strength
2006
16 Citations (Scopus)

"Similarity Trap" in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains

Liu, J., Pan, Y., Ma, B. & Nussinov, R., 1 Dec 2006, In : Structure. 14, 12, p. 1811-1821 11 p.

Research output: Contribution to journalArticle

BRCA1 Protein
Binding Sites
Neoplasm Genes
Proteins
Breast Neoplasms
2005
15 Citations (Scopus)

Study of singlet and triplet 2,6-difluorophenylnitrene by time-resolved infrared spectroscopy

Mandel, S., Liu, J., Hadad, C. M. & Platz, M. S., 31 Mar 2005, In : Journal of Physical Chemistry A. 109, 12, p. 2816-2821 6 p.

Research output: Contribution to journalArticle

Infrared spectroscopy
infrared spectroscopy
products
photochemical reactions
ambient temperature
31 Citations (Scopus)

The reaction of triplet nitrenes with oxygen: A computational study

Liu, J., Hadad, C. M. & Platz, M. S., 17 Feb 2005, In : Organic Letters. 7, 4, p. 549-552 4 p.

Research output: Contribution to journalArticle

carbenes
Discrete Fourier transforms
Oxygen
trends
oxygen
2004
68 Citations (Scopus)

A comparison of acetyl- and methoxycarbonylnitrenes by computational methods and a laser flash photolysis study of benzoylnitrene

Liu, J., Mandel, S., Hadad, C. M. & Platz, M. S., 10 Dec 2004, In : Journal of Organic Chemistry. 69, 25, p. 8583-8593 11 p.

Research output: Contribution to journalArticle

Azides
Photolysis
Computational methods
Lasers
Ground state