Personal information

Verified email addresses

United States, China

Activities

Employment (3)

OpenEye Scientific Software Inc: Santa Fe, New Mexico, US

2022-01-01 to present | Scientific Developer (Enhanced Sampling)
Employment
Source: Self-asserted source
She Zhang

OpenEye Scientific Software Inc: Santa Fe, NM, US

2020-08-26 to 2021-12-31 | Postdoc Research Associate (Biomodeling)
Employment
Source: Self-asserted source
She Zhang

Jiangsu Simcere Pharmaceutical Research Company Ltd: Nanjing, Jiangsu, CN

2014-01-10 to 2014-06-31 | Researcher (Biopharmaceuticals)
Employment
Source: Self-asserted source
She Zhang

Education and qualifications (2)

University of Pittsburgh School of Medicine: Pittsburgh, PA, US

2015-09-01 to 2020-04-20 | PhD (Computational and Systems Biology)
Education
Source: Self-asserted source
She Zhang

Nanjing University of Chinese Medicine School of Pharmacy: Nanjing, Jiangsu, CN

2010-09-01 to 2014-06-30 | B.S. (Biopharmaceuticals)
Education
Source: Self-asserted source
She Zhang

Works (25)

Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRAS G12D

Journal of Chemical Information and Modeling
2024-11-11 | Journal article
Contributors: Neha Vithani; She Zhang; Jeffrey P. Thompson; Lara A. Patel; Alex Demidov; Junchao Xia; Alexander Balaeff; Ahmet Mentes; Yelena A. Arnautova; Anna Kohlmann et al.
Source: check_circle
Crossref

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]

Living Journal of Computational Molecular Science
2022 | Journal article
Contributors: Anthony T. Bogetti; Jeremy M. G. Leung; John D. Russo; She Zhang; Jeff P. Thompson; Ali S. Saglam; Dhiman Ray; Rhea C. Abraham; James R. Faeder; Ioan Andricioaei et al.
Source: check_circle
Crossref

Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow

PLoS Computational Biology
2022 | Journal article
EID:

2-s2.0-85131802922

Part of ISSN: 15537358 1553734X
Contributors: Acar, O.; Zhang, S.; Bahar, I.; Carvunis, A.-R.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1]

2022-10-07 | Preprint
Contributors: Anthony T. Bogetti; Jeremy M. G. Leung; John D. Russo; She Zhang; Jeff P. Thompson; Ali S. Saglam; Dhiman Ray; Rhea C. Abraham; James R. Faeder; Ioan Andricioaei et al.
Source: check_circle
Crossref

Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories

Journal of Chemical Information and Modeling
2022-04-25 | Journal article
Contributors: She Zhang; Jeff P. Thompson; Junchao Xia; Anthony T. Bogetti; Forrest York; A. Geoffrey Skillman; Lillian T. Chong; David N. LeBard
Source: check_circle
Crossref
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WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications

Journal of Chemical Theory and Computation
2022-02-08 | Journal article
Contributors: John D. Russo; She Zhang; Jeremy M. G. Leung; Anthony T. Bogetti; Jeff P. Thompson; Alex J. DeGrave; Paul A. Torrillo; A. J. Pratt; Kim F. Wong; Junchao Xia et al.
Source: check_circle
Crossref
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Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow

bioRxiv
2021 | Other
EID:

2-s2.0-85110653444

Part of ISSN: 26928205
Contributors: Acar, O.; Zhang, S.; Bahar, I.; Carvunis, A.-R.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

HiDeF: identifying persistent structures in multiscale ‘omics data

Genome Biology
2021 | Journal article
EID:

2-s2.0-85098885476

Part of ISSN: 1474760X 14747596
Contributors: Zheng, F.; Zhang, S.; Churas, C.; Pratt, D.; Bahar, I.; Ideker, T.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Mechanistic Insights into Passive Membrane Permeability of Drug-Like Molecules from a Weighted Ensemble of Trajectories

2021-12-20 | Preprint
Contributors: She Zhang; Jeff Thompson; Junchao Xia; Anthony Bogetti; Forrest York; Geoffrey Skillman; Lillian Chong; David LeBard
Source: check_circle
Crossref
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ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution

Bioinformatics
2021-11-05 | Journal article
Contributors: Burak T Kaynak; She Zhang; Ivet Bahar; Pemra Doruker; Lenore Cowen
Source: check_circle
Crossref

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python

Bioinformatics
2021-10-25 | Journal article
Contributors: She Zhang; James M Krieger; Yan Zhang; Cihan Kaya; Burak Kaynak; Karolina Mikulska-Ruminska; Pemra Doruker; Hongchun Li; Ivet Bahar; Lenore Cowen
Source: check_circle
Crossref

Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis

The Journal of Chemical Physics
2021-05-21 | Journal article
Contributors: Yan Zhang; She Zhang; Jianhua Xing; Ivet Bahar
Source: check_circle
Crossref
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ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution

2021-04-18 | Other
Contributors: Burak T. Kaynak; She Zhang; Ivet Bahar; Pemra Doruker
Source: check_circle
Crossref
grade
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Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation

Nucleic Acids Research
2020 | Journal article
EID:

2-s2.0-85082143482

Part of ISSN: 13624962 03051048
Contributors: Zhang, S.; Chen, F.; Bahar, I.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation

Proceedings of the National Academy of Sciences
2020-10-13 | Journal article
Contributors: Mary Hongying Cheng; She Zhang; Rebecca A. Porritt; Magali Noval Rivas; Lisa Paschold; Edith Willscher; Mascha Binder; Moshe Arditi; Ivet Bahar
Source: check_circle
Crossref
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Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

Current Opinion in Structural Biology
2020-06 | Journal article
Contributors: Yan Zhang; Pemra Doruker; Burak Kaynak; She Zhang; James Krieger; Hongchun Li; Ivet Bahar
Source: check_circle
Crossref
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Identifying persistent structures in multiscale ‘omics data

2020-06-17 | Preprint
Contributors: Fan Zheng; She Zhang; Christopher Churas; Dexter Pratt; Ivet Bahar; Trey Ideker
Source: check_circle
Crossref
grade
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An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations

2020-05-21 | Preprint
Contributors: Mary Hongying Cheng; She Zhang; Rebecca A. Porritt; Moshe Arditi; Ivet Bahar
Source: check_circle
Crossref
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Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members

Journal of Chemical Information and Modeling
2019 | Journal article
EID:

2-s2.0-85066862095

Part of ISSN: 1549960X 15499596
Contributors: Mikulska-Ruminska, K.; Shrivastava, I.; Krieger, J.; Zhang, S.; Li, H.; Baylr, H.; Wenzel, S.E.; Vandemark, A.P.; Kagan, V.E.; Bahar, I.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity

Molecular Biology and Evolution
2019 | Journal article
EID:

2-s2.0-85068015587

Part of ISSN: 15371719 07374038
Contributors: Zhang, S.; Li, H.; Krieger, J.M.; Bahar, I.; Ozkan, B.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations

Neuropharmacology
2019 | Journal article
EID:

2-s2.0-85067997747

Part of ISSN: 18737064 00283908
Contributors: Cheng, M.H.; Ponzoni, L.; Sorkina, T.; Lee, J.Y.; Zhang, S.; Sorkin, A.; Bahar, I.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization

Philosophical Transactions of the Royal Society B: Biological Sciences
2018-06-19 | Journal article
Contributors: Luca Ponzoni; She Zhang; Mary Hongying Cheng; Ivet Bahar
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Crossref
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Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

Nucleic Acids Research
2017-03 | Journal article
Part of ISSN: 0305-1048
Contributors: Natalie Sauerwald; She Zhang; Carl Kingsford; Ivet Bahar
Source: Self-asserted source
She Zhang via Crossref Metadata Search
grade
Preferred source (of 2)‎

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

Biophysical Journal
2015 | Journal article
EID:

2-s2.0-84941804038

Part of ISSN: 15420086 00063495
Contributors: Bahar, I.; Cheng, M.H.; Lee, J.Y.; Kaya, C.; Zhang, S.
Source: Self-asserted source
She Zhang via Scopus - Elsevier

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

Biophysical Journal
2015-09-15 | Journal article
Source: Self-asserted source
She Zhang

Peer review (1 review for 1 publication/grant)

Review activity for Communications biology. (1)