A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

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(2018)   JOURNAL OF COMPUTATIONAL CHEMISTRY

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(2018)   LUMINESCENCE

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(2016)   JOURNAL OF COMPUTATIONAL CHEMISTRY

CH–π hydrogen bonds in biological macromolecules

(2014) Motohiro Nishio et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Revealing Origin of Decrease in Potency of Darunavir and Amprenavir against HIV-2 relative to HIV-1 Protease by Molecular Dynamics Simulations

(2014) Jianzhong Chen et al.   Scientific Reports

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

(2013) Dorothee Liebschner et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase

(2013) Yao Fan et al.   BIOCHEMISTRY

Ligand selectivity of estrogen receptors by a molecular dynamics study

(2013) Guodong Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from Molecular Dynamics

(2013) Biswa Ranjan Meher et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model

(2013) Tong Zhu et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

A New Quantum Calibrated Force Field for Zinc–Protein Complex

(2013) Tong Zhu et al.   Journal of Chemical Theory and Computation

A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings

(2013) Jianzhong Chen et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Exploring Transition Pathway and Free-Energy Profile of Large-Scale Protein Conformational Change by Combining Normal Mode Analysis and Umbrella Sampling Molecular Dynamics

(2013) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Stabilization of Different Types of Transition States in a Single Enzyme Active Site: QM/MM Analysis of Enzymes in the Alkaline Phosphatase Superfamily

(2013) Guanhua Hou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for dual inhibitory role of tamarind Kunitz inhibitor (TKI) against factor Xa and trypsin

(2012) Dipak N. Patil et al.   FEBS Journal

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

(2012) Lina Ding et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation

(2012) Tong Zhu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities

(2011) Junji Yamane et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study

(2011) Mahmoud A. A. Ibrahim   Journal of Chemical Information and Modeling

Polarization of Intraprotein Hydrogen Bond Is Critical to Thermal Stability of Short Helix

(2011) Ya Gao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into the Phosphoryl Transfer Mechanism of Cyclin-Dependent Protein Kinases from ab Initio QM/MM Free-Energy Studies

(2011) Gregory K. Smith et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB

(2010) Jinan Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds

(2010) Li L. Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations

(2009) Guo-Dong Hu et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

(2009) Li L. Duan et al.   JOURNAL OF CHEMICAL PHYSICS

Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born−Oppenheimer ab Initio QM/MM Molecular Dynamics Study

(2009) Ruibo Wu et al.   Journal of Chemical Theory and Computation

Determination of the Structure Form of the Fourth Ligand of Zinc in Acutolysin A Using Combined Quantum Mechanical and Molecular Mechanical Simulation

(2009) Emilia L. Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Born−Oppenheimer ab Initio QM/MM Molecular Dynamics Simulations of the Hydrolysis Reaction Catalyzed by Protein Arginine Deiminase 4

(2009) Zhihong Ke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calculation of Protein−Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects

(2009) Pär Söderhjelm et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Theoretical Analysis of Kinetic Isotope Effects on Proton Transfer Reactions between Substituted α-Methoxystyrenes and Substituted Acetic Acids

(2009) Kin-Yiu Wong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantum Mechanical Studies of Residue-Specific Hydrophobic Interactions in p53−MDM2 Binding

(2008) Yun Ding et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS