Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology
MW van der Kamp, AJ Mulholland - Biochemistry, 2013 - ACS Publications
Computational enzymology is a rapidly maturing field that is increasingly integral to
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …
understanding mechanisms of enzyme-catalyzed reactions and their practical applications …
QM/MM methods for biomolecular systems
HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
Advances in methods and algorithms in a modern quantum chemistry program package
Advances in theory and algorithms for electronic structure calculations must be incorporated
into program packages to enable them to become routinely used by the broader chemical …
into program packages to enable them to become routinely used by the broader chemical …
Electrostatic basis for enzyme catalysis
Enzymatic reactions play a fundamentally important role in controlling and performing most
life processes. 1-3 Thus, understanding how enzymes work has both fundamental and …
life processes. 1-3 Thus, understanding how enzymes work has both fundamental and …
Why nature really chose phosphate
SCL Kamerlin, PK Sharma, RB Prasad… - Quarterly reviews of …, 2013 - cambridge.org
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and
maintaining the integrity of the genetic material. On the surface, it would appear to be a …
maintaining the integrity of the genetic material. On the surface, it would appear to be a …
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
SCL Kamerlin, A Warshel - Proteins: Structure, Function, and …, 2010 - Wiley Online Library
Enzymes play a key role in almost all biological processes, accelerating a variety of
metabolic reactions as well as controlling energy transduction, the transcription, and …
metabolic reactions as well as controlling energy transduction, the transcription, and …
Perspective: Defining and quantifying the role of dynamics in enzyme catalysis
A Warshel, RP Bora - The Journal of chemical physics, 2016 - pubs.aip.org
Enzymes control chemical reactions that are key to life processes, and allow them to take
place on the time scale needed for synchronization between the relevant reaction cycles. In …
place on the time scale needed for synchronization between the relevant reaction cycles. In …
How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase
Hybrid quantum mechanical–molecular mechanical (QM/MM) simulations are widely used in
studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the …
studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the …
QM/MM methods for biological systems
HM Senn, W Thiel - Atomistic approaches in modern biology: from …, 2007 - Springer
Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus …
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
H Hu, W Yang - Annu. Rev. Phys. Chem., 2008 - annualreviews.org
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an
accurate and efficient energetic description of complex chemical and biological systems …
accurate and efficient energetic description of complex chemical and biological systems …