Related references
Note: Only part of the references are listed.New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases
Antonija Tomic et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity
Igor Sabljic et al.
PLOS ONE (2018)
Conservation of the conformational dynamics and ligand binding within M49 enzyme family
Sasa Kazazic et al.
RSC ADVANCES (2018)
Keap1-MCM3 interaction is a potential coordinator of molecular machineries of antioxidant response and genomic DNA replication in metazoa
Nele Tamberg et al.
SCIENTIFIC REPORTS (2018)
Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity - a computational study
M. Tomin et al.
MOLECULAR BIOSYSTEMS (2017)
CDK20 interacts with KEAP1 to activate NRF2 and promotes radiochemoresistance in lung cancer cells
Q. Wang et al.
ONCOGENE (2017)
Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly
Apirat Chaikuad et al.
STRUCTURE (2017)
New findings about human dipeptidyl peptidase III based on mutations found in cancer
M. Matovina et al.
RSC ADVANCES (2017)
ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions
D. Franke et al.
JOURNAL OF APPLIED CRYSTALLOGRAPHY (2017)
A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain
Altijana Hromic-Jahjefendic et al.
PLOS ONE (2017)
NRF2 Induction Supporting Breast Cancer Cell Survival Is Enabled by Oxidative Stress-Induced DPP3-KEAP1 Interaction
Kevin Lu et al.
CANCER RESEARCH (2017)
New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations
Sasa Kazazic et al.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2016)
Identification and Characterization of MCM3 as a Kelch-like ECH-associated Protein 1 (KEAP1) Substrate
Kathleen M. Mulvaney et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2016)
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
G. C. P. van Zundert et al.
JOURNAL OF MOLECULAR BIOLOGY (2016)
Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in human DPP III
A. Tomic et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2016)
Molecular effects of cancer-associated somatic mutations on the structural and target recognition properties of Keap1
Halema Khan et al.
BIOCHEMICAL JOURNAL (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding
A. Tomic et al.
MOLECULAR BIOSYSTEMS (2015)
Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents
Hailey R. Bureau et al.
PLOS ONE (2015)
PLUMED 2: New feathers for an old bird
Gareth A. Tribello et al.
COMPUTER PHYSICS COMMUNICATIONS (2014)
Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations
Antonija Tomic et al.
DALTON TRANSACTIONS (2014)
Proteomic Analysis of Ubiquitin Ligase KEAP1 Reveals Associated Proteins That Inhibit NRF2 Ubiquitination
Bridgid E. Hast et al.
CANCER RESEARCH (2013)
The emerging role of the Nrf2-Keap1 signaling pathway in cancer
Melba C. Jaramillo et al.
GENES & DEVELOPMENT (2013)
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Jianjiong Gao et al.
SCIENCE SIGNALING (2013)
Binding of disordered proteins to a protein hub
Elio A. Cino et al.
SCIENTIFIC REPORTS (2013)
Wilms Tumor Gene on X Chromosome (WTX) Inhibits Degradation of NRF2 Protein through Competitive Binding to KEAP1 Protein
Nathan D. Camp et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2012)
Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
Gungor Ozer et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations
Gungor Ozer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
Bill R. Miller et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
PALB2 Interacts with KEAP1 To Promote NRF2 Nuclear Accumulation and Function
Jianglin Ma et al.
MOLECULAR AND CELLULAR BIOLOGY (2012)
Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III
Gustavo A. Bezerra et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
Ethan Cerami et al.
CANCER DISCOVERY (2012)
REFMAC5 for the refinement of macromolecular crystal structures
Garib N. Murshudov et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)
Human Dipeptidyl Peptidase III: the Role of Asn406 in Ligand Binding and Hydrolysis
Jasminka Spoljaric et al.
CROATICA CHEMICA ACTA (2011)
Dipeptidyl peptidase III: a multifaceted oligopeptide N-end cutter
Subhash C. Prajapati et al.
FEBS JOURNAL (2011)
Molecular mechanisms of the Keap1-Nrf2 pathway in stress response and cancer evolution
Keiko Taguchi et al.
GENES TO CELLS (2011)
Structure and dynamics of the kinase IKK-β - A key regulator of the NF-kappa B transcription factor
Munishikha Kalia et al.
JOURNAL OF STRUCTURAL BIOLOGY (2011)
Metadynamics
Alessandro Barducci et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
MolProbity: all-atom structure validation for macromolecular crystallography
Vincent B. Chen et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)
Features and development of Coot
P. Emsley et al.
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)
Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y
Gungor Ozer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
The selective autophagy substrate p62 activates the stress responsive transcription factor Nrf2 through inactivation of Keap1
Masaaki Komatsu et al.
NATURE CELL BIOLOGY (2010)
The Nrf2-Antioxidant Response Element Signaling Pathway and Its Activation by Oxidative Stress
Truyen Nguyen et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2009)
KEAP1 E3 Ligase-Mediated Downregulation of NF-κB Signaling by Targeting IKKβ
Dung-Fang Lee et al.
MOLECULAR CELL (2009)
Structural analysis of the complex of Keap1 with a prothymosin a peptide
Balasundaram Padmanabhan et al.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS (2008)
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
In Suk Joung et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Inference of macromolecular assemblies from crystalline state
Evgeny Krissinel et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Structure of the Keap1: Nrf2 interface provides mechanistic insight into Nrf2 signaling
Shih-Ching Lo et al.
EMBO JOURNAL (2006)
Keap1 recruits Neh2 through binding to ETGE and DLG motifs: Characterization of the two-site molecular recognition model
KI Tong et al.
MOLECULAR AND CELLULAR BIOLOGY (2006)
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
P Raiteri et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Conserved solvent and side-chain interactions in the 1.35 Å structure of the Kelch domain of Keap1
LJ Beamer et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)
Modifying specific cysteines of the electrophile-sensing human Keap1 disrupt binding to the protein is insufficient to Nrf2 domain Neh2
AL Eggler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
PatchDock and SymmDock: servers for rigid and symmetric docking
D Schneidman-Duhovny et al.
NUCLEIC ACIDS RESEARCH (2005)
Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate for proteasomal degradation of Nrf2
A Kobayashi et al.
MOLECULAR AND CELLULAR BIOLOGY (2004)
Nrf2-Keap1 defines a physiologically important stress response mechanism
H Motohashi et al.
TRENDS IN MOLECULAR MEDICINE (2004)
Tumor cytosol dipeptidyl peptidase III activity is increased with histological aggressiveness of ovarian primary carcinomas
S Simaga et al.
GYNECOLOGIC ONCOLOGY (2003)
Keap1-null mutation leads to postnatal lethality due to constitutive Nrf2 activation
N Wakabayashi et al.
NATURE GENETICS (2003)
Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA)
A Bergmann et al.
JOURNAL OF APPLIED CRYSTALLOGRAPHY (2000)