Search Results - "Journal of chemical theory and computation"

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS by Valdés-Tresanco, Mario S, Valdés-Tresanco, Mario E, Valiente, Pedro A, Moreno, Ernesto

“…Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has…”
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OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space by Lu, Chao, Wu, Chuanjie, Ghoreishi, Delaram, Chen, Wei, Wang, Lingle, Damm, Wolfgang, Ross, Gregory A, Dahlgren, Markus K, Russell, Ellery, Von Bargen, Christopher D, Abel, Robert, Friesner, Richard A, Harder, Edward D

“…We report on the development and validation of the OPLS4 force field. OPLS4 builds upon our previous work with OPLS3e to improve model accuracy on challenging…”
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GFN2-xTBAn Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions by Bannwarth, Christoph, Ehlert, Sebastian, Grimme, Stefan

“…An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction…”
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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,…”
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OpenMolcas: From Source Code to Insight by Fdez. Galván, Ignacio, Vacher, Morgane, Alavi, Ali, Angeli, Celestino, Aquilante, Francesco, Autschbach, Jochen, Bao, Jie J, Bokarev, Sergey I, Bogdanov, Nikolay A, Carlson, Rebecca K, Chibotaru, Liviu F, Creutzberg, Joel, Dattani, Nike, Delcey, Mickaël G, Dong, Sijia S, Dreuw, Andreas, Freitag, Leon, Frutos, Luis Manuel, Gagliardi, Laura, Gendron, Frédéric, Giussani, Angelo, González, Leticia, Grell, Gilbert, Guo, Meiyuan, Hoyer, Chad E, Johansson, Marcus, Keller, Sebastian, Knecht, Stefan, Kovačević, Goran, Källman, Erik, Li Manni, Giovanni, Lundberg, Marcus, Ma, Yingjin, Mai, Sebastian, Malhado, João Pedro, Malmqvist, Per Åke, Marquetand, Philipp, Mewes, Stefanie A, Norell, Jesper, Olivucci, Massimo, Oppel, Markus, Phung, Quan Manh, Pierloot, Kristine, Plasser, Felix, Reiher, Markus, Sand, Andrew M, Schapiro, Igor, Sharma, Prachi, Stein, Christopher J, Sørensen, Lasse Kragh, Truhlar, Donald G, Ugandi, Mihkel, Ungur, Liviu, Valentini, Alessio, Vancoillie, Steven, Veryazov, Valera, Weser, Oskar, Wesołowski, Tomasz A, Widmark, Per-Olof, Wouters, Sebastian, Zech, Alexander, Zobel, J. Patrick, Lindh, Roland

“…In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already…”
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OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules by Roos, Katarina, Wu, Chuanjie, Damm, Wolfgang, Reboul, Mark, Stevenson, James M, Lu, Chao, Dahlgren, Markus K, Mondal, Sayan, Chen, Wei, Wang, Lingle, Abel, Robert, Friesner, Richard A, Harder, Edward D

“…Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by…”
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PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges by Unke, Oliver T, Meuwly, Markus

“…In recent years, machine learning (ML) methods have become increasingly popular in computational chemistry. After being trained on appropriate ab initio…”
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Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations by Grimme, Stefan

“…The semiempirical tight-binding based quantum chemistry method GFN2-xTB is used in the framework of meta-dynamics (MTD) to globally explore chemical compound,…”
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Generalized Unitary Coupled Cluster Wave functions for Quantum Computation by Lee, Joonho, Huggins, William J, Head-Gordon, Martin, Whaley, K. Birgitta

“…We introduce a unitary coupled-cluster (UCC) ansatz termed k-UpCCGSD that is based on a family of sparse generalized doubles operators, which provides an…”
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Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability by Parrish, Robert M, Burns, Lori A, Smith, Daniel G. A, Simmonett, Andrew C, DePrince, A. Eugene, Hohenstein, Edward G, Bozkaya, Uğur, Sokolov, Alexander Yu, Di Remigio, Roberto, Richard, Ryan M, Gonthier, Jérôme F, James, Andrew M, McAlexander, Harley R, Kumar, Ashutosh, Saitow, Masaaki, Wang, Xiao, Pritchard, Benjamin P, Verma, Prakash, Schaefer, Henry F, Patkowski, Konrad, King, Rollin A, Valeev, Edward F, Evangelista, Francesco A, Turney, Justin M, Crawford, T. Daniel, Sherrill, C. David

“…Psi4 is an ab initio electronic structure program providing methods such as Hartree–Fock, density functional theory, configuration interaction, and…”
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A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86) by Grimme, Stefan, Bannwarth, Christoph, Shushkov, Philip

“…We propose a novel, special purpose semiempirical tight binding (TB) method for the calculation of structures, vibrational frequencies, and noncovalent…”
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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design by Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J

“…Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation…”
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Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods by Ehlert, Sebastian, Stahn, Marcel, Spicher, Sebastian, Grimme, Stefan

“…We present a robust and efficient method to implicitly account for solvation effects in modern semiempirical quantum mechanics and force fields. A…”
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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…”
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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field by Lee, Jumin, Cheng, Xi, Swails, Jason M, Yeom, Min Sun, Eastman, Peter K, Lemkul, Justin A, Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S, Case, David A, Brooks, Charles L, MacKerell, Alexander D, Klauda, Jeffery B, Im, Wonpil

“…Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. 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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SchNetPack: A Deep Learning Toolbox For Atomistic Systems by Schütt, K. T, Kessel, P, Gastegger, M, Nicoli, K. A, Tkatchenko, A, Müller, K.-R

“…SchNetPack is a toolbox for the development and application of deep neural networks that predict potential energy surfaces and other quantum-chemical…”
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CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans by Lee, Jumin, Patel, Dhilon S, Ståhle, Jonas, Park, Sang-Jun, Kern, Nathan R, Kim, Seonghoon, Lee, Joonseong, Cheng, Xi, Valvano, Miguel A, Holst, Otto, Knirel, Yuriy A, Qi, Yifei, Jo, Sunhwan, Klauda, Jeffery B, Widmalm, Göran, Im, Wonpil

“…Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS),…”
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Tinker 8: Software Tools for Molecular Design by Rackers, Joshua A, Wang, Zhi, Lu, Chao, Laury, Marie L, Lagardère, Louis, Schnieders, Michael J, Piquemal, Jean-Philip, Ren, Pengyu, Ponder, Jay W

“…The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable…”
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Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error by Faber, Felix A, Hutchison, Luke, Huang, Bing, Gilmer, Justin, Schoenholz, Samuel S, Dahl, George E, Vinyals, Oriol, Kearnes, Steven, Riley, Patrick F, von Lilienfeld, O. Anatole

“…We investigate the impact of choosing regressors and molecular representations for the construction of fast machine learning (ML) models of 13 electronic…”
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