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- David S Cerutti, Robert Duke, Peter L Freddolino, Hao Fan, Terry P Lybrand
- Journal of chemical theory and computation
- 2008

We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in many segments, it is sometimes possible to have a repeating sequence of pseudorandom numbers enter the calcuation. We show that, if the sequence repeats rapidly, the resulting artifacts can quickly… (More)

- Pawel A Janowski, David S Cerutti, James Holton, David A Case
- Journal of the American Chemical Society
- 2013

Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in X-ray diffraction data. We present here 9.6 μs of dynamics in a small helical peptide crystal with 36 independent copies of the unit cell. The average simulation structure agrees with experiment to… (More)

- Tushar Jain, David S Cerutti, J Andrew McCammon
- Protein science : a publication of the Protein…
- 2006

Prediction of side-chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an advanced Monte Carlo sampling strategy for predicting side-chain conformations. Our method is based on a cooperative rearrangement of atoms that belong to a group of neighboring side-chains. This… (More)

- Loren Baugh, Isolde Le Trong, +4 authors Terry P Lybrand
- Biochemistry
- 2010

We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed.… (More)

- Edward Harder, Wolfgang Damm, +13 authors Richard A Friesner
- Journal of chemical theory and computation
- 2016

The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native… (More)

- David S Cerutti, Julia E Rice, William C Swope, David A Case
- The journal of physical chemistry. B
- 2013

We have developed the IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water. The method involves iterative cycles of molecular dynamics simulations to estimate the water charge density around the solute of interest, followed by quantum mechanical calculations at the MP2/cc-pV(T+d)Z… (More)

- David S Cerutti, Nathan A Baker, J Andrew McCammon
- The Journal of chemical physics
- 2007

The solvent reaction field potential of an uncharged protein immersed in simple point charge/extended explicit solvent was computed over a series of molecular dynamics trajectories, in total 1560 ns of simulation time. A finite, positive potential of 13-24 kbTec(-1) (where T=300 K), dependent on the geometry of the solvent-accessible surface, was observed… (More)

- David S Cerutti, Lynn F Ten Eyck, J Andrew McCammon
- Journal of chemical theory and computation
- 2005

We have formulated the Energy by Linear Superposition of Corrections Approximation (ELSCA) for estimating the electrostatic and apolar solvation energy of bringing two proteins into close proximity or into contact as defined by the linearized Poisson-Boltzmann model and a linear function of the solvent-accessible surface area. ELSCA utilizes potentials of… (More)

- David S Cerutti, Robert E Duke, Thomas A Darden, Terry P Lybrand
- Journal of chemical theory and computation
- 2009

We draw on an old technique for improving the accuracy of mesh-based field calculations to extend the popular Smooth Particle Mesh Ewald (SPME) algorithm as the Staggered Mesh Ewald (StME) algorithm. StME improves the accuracy of computed forces by up to 1.2 orders of magnitude and also reduces the drift in system momentum inherent in the SPME method by… (More)

- David S Cerutti, Peter L Freddolino, Robert E Duke, David A Case
- The journal of physical chemistry. B
- 2010

We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 Å) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the… (More)