All-atom empirical potential for molecular modeling and dynamics studies of proteins.
- Alexander D. MacKerell, D. Bashford, M. Karplus
- ChemistryJournal of Physical Chemistry B
- 14 April 1998
The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
CHARMM: The biomolecular simulation program
- B. Brooks, C. Brooks, M. Karplus
- ChemistryJournal of Computational Chemistry
- 30 July 2009
An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
The calculation of the potential of mean force using computer simulations
- B. Roux
- Chemistry
- 2 September 1995
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
- James C. Phillips, David J. Hardy, E. Tajkhorshid
- Computer ScienceJournal of Chemical Physics
- 28 July 2020
The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
Energetics of ion conduction through the K+ channel
- S. Bernèche, B. Roux
- BiologyNature
- 1 November 2001
It is found that ion conduction involves transitions between two main states, with two and three K+ ions occupying the selectivity filter, respectively; this process is reminiscent of the ‘knock-on’ mechanism proposed by Hodgkin and Keynes in 1955.
Molecular determinants of gating at the potassium-channel selectivity filter
- J. Cordero-Morales, L. G. Cuello, E. Perozo
- BiologyNature Structural &Molecular Biology
- 30 March 2006
It is shown that in the potassium channel KcsA, proton-dependent activation is followed by an inactivation process similar to C-type inactivation, and this process is suppressed by an E71A mutation in the pore helix, establishing a mechanistic basis for the role of the selectivity filter during channel activation and inactivation.
CHARMM: The Energy Function and Its Parameterization
- Alexander D. MacKerell, B. Brooks, M. Karplus
- Physics
- 15 April 2002
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
- S. Noskov, S. Bernèche, B. Roux
- BiologyNature
- 14 October 2004
Molecular dynamics simulations for the potassium channel KcsA show that the carbonyl groups coordinating the ion in the narrow pore are indeed very dynamic (‘liquid-like’) and that their intrinsic electrostatic properties control ion selectivity.
Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
An approach is developed to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster. A rigorous theoretical formulation is given for…
Structural basis for the coupling between activation and inactivation gates in K+ channels
- L. G. Cuello, V. Jogini, E. Perozo
- BiologyNature
- 8 July 2010
This work identifies the mechanistic principles by which movements on the inner bundle gate trigger conformational changes at the selectivity filter, leading to the non-conductive C-type inactivated state and proposes that side-chain rearrangements at position 103 mechanically couple activation and inactivation in K+ channels.
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