Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8

Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair

(2020) Sodiq O. Waheed et al.   ACS Central Science

Unpicking the Cause of Stereoselectivity in Actinorhodin Ketoreductase Variants with Atomistic Simulations

(2019) Stefano A. Serapian et al.   ACS Catalysis

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

(2019) Bodee Nutho et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cooperativity and flexibility in enzyme evolution

(2018) Anna Pabis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase

(2018) Insung Na et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

(2018) Shuichiro Tsukamoto et al.   JOURNAL OF CHEMICAL PHYSICS

Histone Deacetylase Inhibitors as Anticancer Drugs

(2017) Tomas Eckschlager et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

HDAC8 substrate selectivity is determined by long- and short-range interactions leading to enhanced reactivity for full-length histone substrates compared with peptides

(2017) Carol Ann Castañeda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Exploring the Active Center of the LSD1/CoREST Complex by Molecular Dynamics Simulation Utilizing Its Co-crystallized Co-factor Tetrahydrofolate as a Probe

(2017) Waleed A. Zalloum et al.   Journal of Chemical Information and Modeling

Conformational Dynamics of Matrix Metalloproteinase-1·Triple-Helical Peptide Complexes

(2017) Tatyana G. Karabencheva-Christova et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QSAR modeling to design selective histone deacetylase 8 (HDAC8) inhibitors

(2016) Guang Ping Cao et al.   ARCHIVES OF PHARMACAL RESEARCH

Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8

(2016) Nicholas J. Porter et al.   BIOCHEMISTRY

Inhibition of histone deacetylases in cancer therapy: lessons from leukaemia

(2016) Elena Ceccacci et al.   BRITISH JOURNAL OF CANCER

Transcriptional Selectivity of Epigenetic Therapy in Cancer

(2016) Takahiro Sato et al.   CANCER RESEARCH

Targeting histone deacetylase 8 as a therapeutic approach to cancer and neurodegenerative diseases

(2016) Alokta Chakrabarti et al.   Future Medicinal Chemistry

Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region

(2016) Garima Jindal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Epigenetics and Human Disease

(2016) Huda Y. Zoghbi et al.   Cold Spring Harbor Perspectives in Biology

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li et al.   Journal of Chemical Theory and Computation

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ion models commonly used in biomolecular simulations

(2015) Maria T. Panteva et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Histone Deacetylase Inhibitors in Clinical Studies as Templates for New Anticancer Agents

(2015) Madhusoodanan Mottamal et al.   MOLECULES

Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays

(2015) Zainab Noor et al.   PLoS One

HDAC8: a multifaceted target for therapeutic interventions

(2015) Alokta Chakrabarti et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

QM/MM Calculations Revealing the Resting and Catalytic States in Zinc-Dependent Medium-Chain Dehydrogenases/Reductases

(2015) Gaurao V. Dhoke et al.   ACS Catalysis

QM/MM MD Simulations on the Enzymatic Pathway of the Human Flap Endonuclease (hFEN1) Elucidating Common Cleavage Pathways to RNase H Enzymes

(2015) Jacopo Sgrignani et al.   ACS Catalysis

Targeting Epigenetics in Drug Discovery

(2014) Antonello Mai   ChemMedChem

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

(2014) Pengfei Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Epigenetic targets and drug discovery

(2014) Yanli Liu et al.   PHARMACOLOGY & THERAPEUTICS

Erasers of Histone Acetylation: The Histone Deacetylase Enzymes

(2014) E. Seto et al.   Cold Spring Harbor Perspectives in Biology

Specificity in Transition State Binding: The Pauling Model Revisited

(2013) Tina L. Amyes et al.   BIOCHEMISTRY

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

An extensible interface for QM/MM molecular dynamics simulations with AMBER

(2013) Andreas W. Götz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Histone Deacetylases

(2013) Sabnam Parbin et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Loop Interactions and Dynamics Tune the Enzymatic Activity of the Human Histone Deacetylase 8

(2013) Micha B. A. Kunze et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A steered molecular dynamics mediated hit discovery for histone deacetylases

(2013) Subha Kalyaanamoorthy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

In SilicoScreening and Molecular Dynamics Simulation of Disease-Associated nsSNP in TYRP1 Gene and Its Structural Consequences in OCA3

(2013) Balu Kamaraj et al.   Biomed Research International

Importance and Limitations of Chemotherapy Among the Available Treatments for Gastrointestinal Tumours

(2012) Jose Marin et al.   Anti-Cancer Agents in Medicinal Chemistry

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Molecular Dynamics Simulation Study Explaining Inhibitor Selectivity in Different Class of Histone Deacetylases

(2012) Sundarapandian Thangapandian et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations

(2012) Subha Kalyaanamoorthy et al.   Journal of Chemical Information and Modeling

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain

(2012) Antje Wolf et al.   JOURNAL OF MOLECULAR MODELING

Roles of histone deacetylases in epigenetic regulation: emerging paradigms from studies with inhibitors

(2012) Geneviève P Delcuve et al.   Clinical Epigenetics

A study on the flexibility of enzyme active sites

(2011) Yi-Zhong Weng et al.   BMC BIOINFORMATICS

Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes

(2011) Patrick M Lombardi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic Molecules

(2011) Martin Korth et al.   Journal of Chemical Theory and Computation

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions

(2010) Ruibo Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The folding and unfolding of eukaryotic chromatin

(2009) Andrew Bassett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Histone Deacetylase Inhibitors in Cancer Therapy

(2009) Andrew A. Lane et al.   JOURNAL OF CLINICAL ONCOLOGY

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors†,‡

(2008) Daniel P. Dowling et al.   BIOCHEMISTRY

Histone Deacetylase Inhibitors as Novel Anti-Cancer Therapeutics

(2008) Xiang-Jiao Yang et al.   Current Oncology

Application of the PM6 method to modeling proteins

(2008) James J. P. Stewart   JOURNAL OF MOLECULAR MODELING

Targeted Cancer Therapy: Conferring Specificity to Cytotoxic Drugs

(2007) Ravi V. J. Chari   ACCOUNTS OF CHEMICAL RESEARCH