• Publications
  • Influence
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balanceExpand
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CHARMM: The biomolecular simulation program
TLDR
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. Expand
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How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations
Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in theExpand
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Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions
  • Yingjie Wang, M. Liu, J. Gao
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences
  • 5 June 2020
Significance Enhanced receptor binding by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to contribute to the highly contagious transmission rate of coronavirus diseaseExpand
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Quantum mechanical methods for enzyme kinetics.
  • J. Gao, D. Truhlar
  • Chemistry, Medicine
  • Annual review of physical chemistry
  • 28 November 2003
This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects:Expand
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A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations
A generalized hybrid orbital (GHO) method has been developed at the semiempirical level in combined quantum mechanical and molecular mechanical (QM/MM) calculations. In this method, a set of hybridExpand
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Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.
  • N. Wu, Y. Mo, J. Gao, E. Pai
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences…
  • 29 February 2000
Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in biosynthesis of pyrimidine nucleotides. As part of aExpand
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The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure*
Background: The interaction between methionine and aromatic residues in protein complexes is poorly understood. Results: The Met-aromatic motif is prevalent in known protein structures and stabilizesExpand
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Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.
6.2. Reactive Flux Method 3156 6.3. Model Theories 3156 6.4. Survey 3156 7. Applications 3157 7.1. Yeast Enolase 3157 7.2. Triosephosphate Isomerase 3157 7.3. Methylamine Dehydrogenase 3158 7.4.Expand
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The incorporation of quantum effects in enzyme kinetics modeling.
We present an overview of new procedures for including quantum mechanical effects in enzyme kinetics. Quantum effects are included in three ways: (1) The electronic structure of the atoms in theExpand
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