Search Results - "Cerutti, David S"

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features by Lee, Tai-Sung, Cerutti, David S, Mermelstein, Dan, Lin, Charles, LeGrand, Scott, Giese, Timothy J, Roitberg, Adrian, Case, David A, Walker, Ross C, York, Darrin M

“…We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the…”
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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins by Harder, Edward, Damm, Wolfgang, Maple, Jon, Wu, Chuanjie, Reboul, Mark, Xiang, Jin Yu, Wang, Lingle, Lupyan, Dmitry, Dahlgren, Markus K, Knight, Jennifer L, Kaus, Joseph W, Cerutti, David S, Krilov, Goran, Jorgensen, William L, Abel, Robert, Friesner, Richard A

“…The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version…”
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Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model by Debiec, Karl T, Cerutti, David S, Baker, Lewis R, Gronenborn, Angela M, Case, David A, Chong, Lillian T

“…We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving…”
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Molecular dynamics simulations of macromolecular crystals by Cerutti, David S., Case, David A.

“…The structures of biological macromolecules would not be known to their present extent without X‐ray crystallography. Most simulations of globular proteins in…”
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Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex by Cerutti, David S, Le Trong, Isolde, Stenkamp, Ronald E, Lybrand, Terry P

“…A 250 ns molecular dynamics simulation of the biotin-liganded streptavidin crystal lattice, including cryoprotectant molecules and crystallization salts, is…”
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Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations by Cerutti, David S, Trong, Isolde Le, Stenkamp, Ronald E, Lybrand, Terry P

“…We present a 250 ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously…”
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AmberTools by Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, Andreas W., Gohlke, Holger, Izadi, Saeed, Kasavajhala, Koushik, Kaymak, Mehmet C., King, Edward, Kurtzman, Tom, Lee, Tai-Sung, Li, Pengfei, Liu, Jian, Luchko, Tyler, Luo, Ray, Manathunga, Madushanka, Machado, Matias R., Nguyen, Hai Minh, O’Hearn, Kurt A., Onufriev, Alexey V., Pan, Feng, Pantano, Sergio, Qi, Ruxi, Rahnamoun, Ali, Risheh, Ali, Schott-Verdugo, Stephan, Shajan, Akhil, Swails, Jason, Wang, Junmei, Wei, Haixin, Wu, Xiongwu, Wu, Yongxian, Zhang, Shi, Zhao, Shiji, Zhu, Qiang, Cheatham, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.

“…AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within…”
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Second-Contact Shell Mutation Diminishes Streptavidin–Biotin Binding Affinity through Transmitted Effects on Equilibrium Dynamics by Baugh, Loren, Le Trong, Isolde, Cerutti, David S, Mehta, Nital, Gülich, Susanne, Stayton, Patrick S, Stenkamp, Ronald E, Lybrand, Terry P

“…We report a point mutation in the second contact shell of the high-affinity streptavidin–biotin complex that appears to reduce binding affinity through…”
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Configurational‐bias sampling technique for predicting side‐chain conformations in proteins by Jain, Tushar, Cerutti, David S., McCammon, J. Andrew

“…Prediction of side‐chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an…”
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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins by Cerutti, David S, Swope, William C, Rice, Julia E, Case, David A

“…We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the…”
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Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization by Cerutti, David S, Rice, Julia E, Swope, William C, Case, David A

“…We have developed the IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water. The…”
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Fast Implementation of the Nudged Elastic Band Method in AMBER by Ghoreishi, Delaram, Cerutti, David S, Fallon, Zachary, Simmerling, Carlos, Roitberg, Adrian E

“…We present a fast implementation of the nudged elastic band (NEB) method into the particle mesh Ewald molecular dynamics module of the Amber software package…”
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Peptide Crystal Simulations Reveal Hidden Dynamics by Janowski, Pawel A, Cerutti, David S, Holton, James, Case, David A

“…Molecular dynamics simulations of biomolecular crystals at atomic resolution have the potential to recover information on dynamics and heterogeneity hidden in…”
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Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility by Cerutti, David S, Duke, Robert E, Darden, Thomas A, Lybrand, Terry P

“…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…”
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On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge by Bansal, Nupur, Zheng, Zheng, Cerutti, David S., Merz, Kenneth M.

“…We review our performance in the SAMPL5 challenge for predicting host–guest binding affinities using the movable type (MT) method. The challenge included three…”
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Alchemical prediction of hydration free energies for SAMPL by Mobley, David L., Liu, Shaui, Cerutti, David S., Swope, William C., Rice, Julia E.

“…Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations…”
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Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models by Cerutti, David S, Freddolino, Peter L, Duke, Robert E, Case, David A

“…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…”
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A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics by Cerutti, David S, Duke, Robert, Freddolino, Peter L, Fan, Hao, Lybrand, Terry P

“…We report a serious problem associated with a number of current implementations of Andersen and Langevin dynamics algorithms. When long simulations are run in…”
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Rapid Estimation of Solvation Energy for Simulations of Protein−Protein Association by Cerutti, David S, Ten Eyck, Lynn F, McCammon, J. Andrew

“…We have formulated the Energy by Linear Superposition of Corrections Approximation (ELSCA) for estimating the electrostatic and apolar solvation energy of…”
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Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem by Cerutti, David S, Case, David A

“…We present a new method for decomposing the one convolution required by standard Particle−Particle Particle-Mesh (P3M) electrostatic methods into a series of…”
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