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51

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

Melvin, Ryan L., Godwin, Ryan C., Xiao, Jiajie, Thompson, William G., Berenhaut, Kenneth S., Salsbury, Freddie R.

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 2.82 MB

english, 2016

52

Autoinhibitory mechanisms of ERG studied by molecular dynamics simulations

Lu, Yan, Salsbury, Freddie R.

Journal:

Year:

2015

Language:

english

File:

PDF, 6.12 MB

english, 2015

53

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator)

Godwin, Ryan C., Melvin, Ryan L., Gmeiner, William H., Salsbury, Freddie R.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.63 MB

english, 2017

54

Experimentally Dissecting the Origins of Peroxiredoxin Catalysis

Nelson, Kimberly J., Perkins, Arden, Van Swearingen, Amanda E.D., Hartman, Steven, Brereton, Andrew E., Parsonage, Derek, Salsbury, Freddie R., Karplus, P. Andrew, Poole, Leslie B.

Journal:

Antioxidants & Redox Signaling

Year:

2017

Language:

english

File:

PDF, 1.61 MB

english, 2017

55

Small static electric field strength promotes aggregation-prone structures in amyloid- β (29-42)

Lu, Yan, Shi, Xiao-Feng, Salsbury, Freddie R., Derreumaux, Philippe

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 4.81 MB

english, 2017

56

All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer

Melvin, Ryan L, Gmeiner, William, Salsbury, Freddie

Journal:

Physical Chemistry Chemical Physics

Year:

2017

Language:

english

File:

PDF, 7.53 MB

english, 2017

57

All-Atom Molecular Dynamics Comparison of Disease-Associated Zinc Fingers

Godwin, Ryan C., Gmeiner, William H., Salsbury, Freddie R.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2017

Language:

english

File:

PDF, 3.03 MB

english, 2017

58

All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic

Melvin, Ryan L., Gmeiner, William H., Salsbury, Freddie R.

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 6.63 MB

english, 2017

59

Mechanistic insights into thrombin's switch between "slow" and "fast" forms

Xiao, Jiajie, Melvin, Ryan L, Salsbury, Freddie

Journal:

Physical Chemistry Chemical Physics

Year:

2017

Language:

english

File:

PDF, 6.52 MB

english, 2017

60

Influence of electric field on the amyloid- β (29-42) peptides embedded in a membrane bilayer

Lu, Yan, Shi, Xiao-Feng, Salsbury, Freddie R., Derreumaux, Philippe

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 6.15 MB

english, 2018

61

Probing Light Chain Mutation Effects on Thrombin via Molecular Dynamics Simulations and Machine Learning

Xiao, Jiajie, Melvin, Ryan L., Salsbury, Freddie R.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2018

Language:

english

File:

PDF, 2.23 MB

english, 2018

62

A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations

Bennion, Brian J., Essiz, Sebnem G., Lau, Edmond Y., Fattebert, Jean-Luc, Emigh, Aiyana, Lightstone, Felice C., Salsbury , Jr, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 1.72 MB

english, 2015

63

Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA

Mena-Ulecia, Karel, Tiznado, William, Caballero, Julio, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 3.39 MB

english, 2015

64

Alpha conotoxin-BuIA globular isomer is a competitive antagonist for oleoyl-L-alpha-lysophosphatidic acid binding to LPAR6; A molecular dynamics study

Younis, Saima, Rashid, Sajid, Salsbury, Freddie

Journal:

Year:

2017

Language:

english

File:

PDF, 16.63 MB

english, 2017

65

Primary Ion Depletion Kinetics (PIDK) Studies as a New Tool for Investigating Chemical Ionization Fragmentation Reactions with PTR-MS

Schuhfried, Erna, Märk, Tilmann D., Biasioli, Franco, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.09 MB

english, 2013

66

Identification of Novel Interacting Partners of Sirtuin6

Polyakova, Oxana, Borman, Satty, Grimley, Rachel, Vamathevan, Jessica, Hayes, Brian, Solari, Roberto, Salsbury, Freddie

Journal:

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

67

Chiral Ruthenium(II) Polypyridyl Complexes: Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity and Cellular Uptake

Yu, Qianqian, Liu, Yanan, Wang, Chuan, Sun, Dongdong, Yang, Xingcheng, Liu, Yanyu, Liu, Jie, Salsbury Jr, Freddie

Journal:

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

68

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

Senter, Evan, Sheikh, Saad, Dotu, Ivan, Ponty, Yann, Clote, Peter, Salsbury, Freddie

Journal:

Year:

2012

Language:

english

File:

PDF, 929 KB

english, 2012

69

Calcium Induced Regulation of Skeletal Troponin — Computational Insights from Molecular Dynamics Simulations

Genchev, Georgi Z., Kobayashi, Tomoyoshi, Lu, Hui, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.69 MB

english, 2013

70

A Quantitative Measure of Electrostatic Perturbation in Holo and Apo Enzymes Induced by Structural Changes

Chakraborty, Sandeep, Salsbury Jr, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 1.18 MB

english, 2013

71

On the Characterization and Software Implementation of General Protein Lattice Models

Bechini, Alessio, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.12 MB

english, 2013

72

Identification, Design and Bio-Evaluation of Novel Hsp90 Inhibitors by Ligand-Based Virtual Screening

Jia, JianMin, Xu, XiaoLi, Liu, Fang, Guo, XiaoKe, Zhang, MingYe, Lu, MengChen, Xu, LiLi, Wei, JinLian, Zhu, Jia, Zhang, ShengLie, Zhang, ShengMiao, Sun, HaoPeng, You, QiDong, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 14.40 MB

english, 2013

73

Mapping Enzymatic Catalysis Using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

Steinmann, Casper, Fedorov, Dmitri G., Jensen, Jan H., Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

74

Interface of the Polarizable Continuum Model of Solvation with Semi-Empirical Methods in the GAMESS Program

Steinmann, Casper, Blædel, Kristoffer L., Christensen, Anders S., Jensen, Jan H., Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 490 KB

english, 2013

75

Computer Simulation of Assembly and Co-operativity of Hexameric AAA ATPases

Le, Doan Tuong-Van, Eckert, Thomas, Woehlke, Günther, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 4.86 MB

english, 2013

76

Interaction between Trehalose and MTHase from Sulfolobus solfataricus Studied by Theoretical Computation and Site-Directed Mutagenesis

Fu, Chien-wei, Wang, Yu-Ping, Fang, Tsuei-Yun, Lin, Thy-Hou, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

77

Computational Study on the Different Ligands Induced Conformation Change of β2 Adrenergic Receptor-Gs Protein Complex

Bai, Qifeng, Zhang, Yang, Ban, Yihe, Liu, Huanxiang, Yao, Xiaojun, Salsbury Jr, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.18 MB

english, 2013

78

Tuning of Thioredoxin Redox Properties by Intramolecular Hydrogen Bonds

Røhr, Åsmund Kjendseth, Hammerstad, Marta, Andersson, K. Kristoffer, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 977 KB

english, 2013

79

Molecular Dynamics Simulations of Water/Mucus Partition Coefficients for Feeding Stimulants in Fish and the Implications for Olfaction

Rygg, Alex D., van Duin, Adri C. T., Craven, Brent A., Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 791 KB

english, 2013

80

Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity

Yan, Zhiqiang, Wang, Jin, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 495 KB

english, 2013

81

Differences in the Binding Affinities of ErbB Family: Heterogeneity in the Prediction of Resistance Mutants

Pereira, Mariana, Verma, Chandra S., Fuentes, Gloria, Salsbury Jr., Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 5.81 MB

english, 2013

82

Structural Insights into Saccharomyces cerevisiae Msh4–Msh5 Complex Function Using Homology Modeling

Rakshambikai, Ramaswamy, Srinivasan, Narayanaswamy, Nishant, Koodali Thazath, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 927 KB

english, 2013

83

Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data

Ferguson, Andrew L., Falkowska, Emilia, Walker, Laura M., Seaman, Michael S., Burton, Dennis R., Chakraborty, Arup K., Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 564 KB

english, 2013

84

Probing the Effect of the Non-Active-Site Mutation Y229W in New Delhi Metallo-β-lactamase-1 by Site-Directed Mutagenesis, Kinetic Studies, and Molecular Dynamics Simulations

Chen, Jiao, Chen, Hui, Shi, Yun, Hu, Feng, Lao, Xingzhen, Gao, Xiangdong, Zheng, Heng, Yao, Wenbing, Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 2.38 MB

english, 2013

85

Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes

Beard, Hege, Cholleti, Anuradha, Pearlman, David, Sherman, Woody, Loving, Kathryn A., Salsbury , Jr, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 1.41 MB

english, 2013

86

A Novel Detection Scheme for High-Resolution Two-Dimensional Spin-Echo Correlated Spectra in Inhomogeneous Fields

Huang, Yuqing, Zhang, Zhiyong, Cai, Shuhui, Chen, Zhong, Salsbury Jr., Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 729 KB

english, 2014

87

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

Christensen, Anders S., Linnet, Troels E., Borg, Mikael, Boomsma, Wouter, Lindorff-Larsen, Kresten, Hamelryck, Thomas, Jensen, Jan H., Salsbury, Freddie

Journal:

Year:

2013

Language:

english

File:

PDF, 1023 KB

english, 2013

88

Computational Study on the Inhibitor Binding Mode and Allosteric Regulation Mechanism in Hepatitis C Virus NS3/4A Protein

Xue, Weiwei, Yang, Ying, Wang, Xiaoting, Liu, Huanxiang, Yao, Xiaojun, Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 3.22 MB

english, 2014

89

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

Dasgupta, Bhaskar, Kasahara, Kota, Kamiya, Narutoshi, Nakamura, Haruki, Kinjo, Akira R., Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 2.12 MB

english, 2014

90

Protonated Form: The Potent Form of Potassium-Competitive Acid Blockers

Luo, Hua-Jun, Deng, Wei-Qiao, Zou, Kun, Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 7.72 MB

english, 2014

91

Exploring the RING-Catalyzed Ubiquitin Transfer Mechanism by MD and QM/MM Calculations

Zhen, Yunmei, Qin, Guangrong, Luo, Cheng, Jiang, Hualiang, Yu, Kunqian, Chen, Guanghui, Salsbury,, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 2.24 MB

english, 2014

92

Computational Investigation of Locked Nucleic Acid (LNA) Nucleotides in the Active Sites of DNA Polymerases by Molecular Docking Simulations

Poongavanam, Vasanthanathan, Madala, Praveen K., Højland, Torben, Veedu, Rakesh N., Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 1.27 MB

english, 2014

93

Computational Prediction and Analysis of Breast Cancer Targets for 6-Methyl-1, 3, 8-Trichlorodibenzofuran

Chitrala, Kumaraswamy Naidu, Yeguvapalli, Suneetha, Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 3.03 MB

english, 2014

94

Estimation of Clustering Parameters Using Gaussian Process Regression

Rigby, Paul, Pizarro, Oscar, Williams, Stefan B., Salsbury, Freddie

Journal:

Year:

2014

Language:

english

File:

PDF, 4.13 MB

english, 2014

95

Effects of the Pathogenic Mutation A117V and the Protective Mutation H111S on the Folding and Aggregation of PrP106-126: Insights from Replica Exchange Molecular Dynamics Simulations

Ning, Lulu, Pan, Dabo, Zhang, Yan, Wang, Shaopeng, Liu, Huanxiang, Yao, Xiaojun, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 6.04 MB

english, 2015

96

An Algorithm for Protein Helix Assignment Using Helix Geometry

Cao, Chen, Xu, Shutan, Wang, Lincong, Salsbury, Jr, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 2.90 MB

english, 2015

97

An Accurate Model for Biomolecular Helices and Its Application to Helix Visualization

Wang, Lincong, Qiao, Hui, Cao, Chen, Xu, Shutan, Zou, Shuxue, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 4.73 MB

english, 2015

98

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation

Moritsugu, Kei, Koike, Ryotaro, Yamada, Kouki, Kato, Hiroaki, Kidera, Akinori, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 3.08 MB

english, 2015

99

Computational Structure-Based De Novo Design of Hypothetical Inhibitors against the Anti- Inflammatory Target COX-2

Dhanjal, Jaspreet Kaur, Sreenidhi, Anith Kumar, Bafna, Khushboo, Katiyar, Shashank Prakash, Goyal, Sukriti, Grover, Abhinav, Sundar, Durai, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 4.45 MB

english, 2015

100

The Mechanism by which 146-N-Glycan Affects the Active Site of Neuraminidase

Liu, Pi, Wang, Zhonghua, Zhang, Lijie, Li, Dongmei, Lin, Jianping, Salsbury, Freddie

Journal:

Year:

2015

Language:

english

File:

PDF, 1.70 MB

english, 2015