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 …

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” …

Advances in methods and algorithms in a modern quantum chemistry program package

Y Shao, LF Molnar, Y Jung, J Kussmann… - Physical Chemistry …, 2006 - pubs.rsc.org
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 …

Electrostatic basis for enzyme catalysis

A Warshel, PK Sharma, M Kato, Y Xiang, H Liu… - Chemical …, 2006 - ACS Publications
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 …

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 …

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 …

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 …

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

HJ Kulik, J Zhang, JP Klinman… - The Journal of Physical …, 2016 - ACS Publications
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 …

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 …

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 …