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1

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

Jiang, Wei, Phillips, James C., Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., Luo, Yun, Schulten, Klaus, Roux, Benoît

Journal:

Computer Physics Communications

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

2

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

Mikolai Fajer, Robert V. Swift, J. Andrew McCammon

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 157 KB

english, 2009

3

Identifying Binding Cooperativity in Protein Kinase a through Community Analysis

Fajer, Mikolai, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

4

Fast and Accurate Calculation of Small Molecule Solvation Free Energies using Replica Exchange Accelerated Molecular Dynamics

Arrar, Mehrnoosh, Sinko, William, Fajer, Mikolai, Agusto, Cesar, Oliveira, F. de, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 35 KB

english, 2012

5

Do Spin Labels Tell the Truth?

Fajer, Peter, Mikolai, Fajer, Zawrotny, Michael, Yang, Wei

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 117 KB

english, 2014

6

ESTRO meetings

Jiang, Wei, Phillips, James C., Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., Luo, Yun, Schulten, Klaus, Roux, Benoît

Journal:

Radiotherapy and Oncology

Year:

1996

Language:

english

File:

PDF, 41 KB

english, 1996

7

Dynamics of the PKA C-Subunit Major Conformational States Using REXAMD

Fajer, Mikolai, Taylor, Susan, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 35 KB

english, 2010

8

Generalized Scalable Multiple Copy Algorithms for Biological Molecular Dynamics Simulations in NAMD

Jiang, Wei, Phillips, James, Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., luo, yun, Schulten, Klaus, roux, benoit

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 44 KB

english, 2014

9

Simulation of the Conformational Transition Pathway for the Activation of Full-Length C-Src Kinase using the String Method

Fajer, Mikolai, Meng, Yilin, Roux, Benoit

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 99 KB

english, 2014

10

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations

Arrar, Mehrnoosh, de Oliveira, Cesar Augusto F., Fajer, Mikolai, Sinko, William, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.08 MB

english, 2013

11

On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations

Rogers, Kathleen E., Ortiz-Sánchez, Juan Manuel, Baron, Riccardo, Fajer, Mikolai, de Oliveira, César Augusto F., McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 4.69 MB

english, 2013

12

Mapping Electron Paramagnetic Resonance Spin Label Conformations by the Simulated Scaling Method

Fajer, Mikolai I., Li, Hongzhi, Yang, Wei, Fajer, Piotr G.

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 372 KB

english, 2007

13

Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State

Khavrutskii, Ilja V., Fajer, Mikolai, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 1.31 MB

english, 2008

14

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

Fajer, Mikolai, Hamelberg, Donald, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 772 KB

english, 2008

15

The Constricted Filter Conformation: A General Property for C-Type Inactivation of Different Potassium Channels?

Li, Jing, Ostmeyer, Jared, Fajer, Mikolai, Roux, Benoit

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 39 KB

english, 2016

16

The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape

Fajer, Mikolai, Meng, Yilin, Roux, Benoit

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

17

Simulated scaling method for localized enhanced sampling and simultaneous “alchemical” free energy simulations: A general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations

Li, Hongzhi, Fajer, Mikolai, Yang, Wei

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 1.40 MB

english, 2007

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