Search Results - "Kasavajhala, Koushik"

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB by Maier, James A, Martinez, Carmenza, Kasavajhala, Koushik, Wickstrom, Lauren, Hauser, Kevin E, Simmerling, Carlos

“…Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein…”
Get full text

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution by Tian, Chuan, Kasavajhala, Koushik, Belfon, Kellon A. A, Raguette, Lauren, Huang, He, Migues, Angela N, Bickel, John, Wang, Yuzhang, Pincay, Jorge, Wu, Qin, Simmerling, Carlos

“…Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation,…”
Get full text

Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State by Goyal, Siddharth, Chattopadhyay, Aditya, Kasavajhala, Koushik, Priyakumar, U. Deva

“…A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states…”
Get full text

Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations by Kasavajhala, Koushik, Simmerling, Carlos

“…Generating precise ensembles is commonly a prerequisite to understand the energetics of biological processes using Molecular Dynamics (MD) simulations…”
Get full text

Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations by Kasavajhala, Koushik, Lam, Kenneth, Simmerling, Carlos

“…Temperature replica exchange molecular dynamics (REMD) is a widely used enhanced sampling method for accelerating biomolecular simulations. During the past 2…”
Get full text

Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir by Lam, Kenneth, Kasavajhala, Koushik, Gunasekera, Sarah, Simmerling, Carlos

“…RNA is a key participant in many biological processes, but studies of RNA using computer simulations lag behind those of proteins, largely due to…”
Get full text

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…”
Get full text

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery by Zhang, Yuqi, Vass, Marton, Shi, Da, Abualrous, Esam, Chambers, Jennifer M., Chopra, Nikita, Higgs, Christopher, Kasavajhala, Koushik, Li, Hubert, Nandekar, Prajwal, Sato, Hideyuki, Miller, Edward B., Repasky, Matthew P., Jerome, Steven V.

“…The recently developed AlphaFold2 (AF2) algorithm predicts proteins’ 3D structures from amino acid sequences. The open AlphaFold protein structure database…”
Get full text

Using Structure Reservoirs to Accelerate Biomolecular Simulations by Kasavajhala, Koushik

“…Development of accurate potential energy functions and advances in computing hardware have made molecular dynamics simulations an indispensable tool for…”
Get full text

ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution by Tian, Chuan, Kasavajhala, Koushik, Belfon, Kellon A. A., Raguette, Lauren, Huang, He, Migues, Angela N., Bickel, John, Wang, Yuzhang, Pincay, Jorge, Wu, Qin, Simmerling, Carlos

“…Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation,…”
Get full text

Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution by Kasavajhala, Koushik, Bikkina, Swetha, Patil, Indrajit, MacKerell, Alexander D, Priyakumar, U. Deva

“…Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in…”
Get full text

Extracting representative structures from protein conformational ensembles: Choosing Accurate Structures from Protein Ensembles by Perez, Alberto, Roy, Arijit, Kasavajhala, Koushik, Wagaman, Amy, Dill, Ken A., MacCallum, Justin L.

Get full text

Extracting representative structures from protein conformational ensembles by Perez, Alberto, Roy, Arijit, Kasavajhala, Koushik, Wagaman, Amy, Dill, Ken A., MacCallum, Justin L.

“…ABSTRACT A large number of methods generate conformational ensembles of biomolecules. Often one structure is selected to be representative of the whole…”
Get full text