Suchergebnisse - "Journal of chemical theory and computation"

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS von 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 von 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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ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution von 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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GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions von 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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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry von Li Manni, Giovanni, Fdez Galván, Ignacio, Alavi, Ali, Aleotti, Flavia, Aquilante, Francesco, Autschbach, Jochen, Avagliano, Davide, Baiardi, Alberto, Bao, Jie J, Battaglia, Stefano, Birnoschi, Letitia, Blanco-González, Alejandro, Bokarev, Sergey I, Broer, Ria, Cacciari, Roberto, Calio, Paul B, Carlson, Rebecca K, Carvalho Couto, Rafael, Cerdán, Luis, Chibotaru, Liviu F, Chilton, Nicholas F, Church, Jonathan Richard, Conti, Irene, Coriani, Sonia, Cuéllar-Zuquin, Juliana, Daoud, Razan E, Dattani, Nike, Decleva, Piero, de Graaf, Coen, Delcey, Mickaël G, De Vico, Luca, Dobrautz, Werner, Dong, Sijia S, Feng, Rulin, Ferré, Nicolas, Filatov Gulak, Michael, Gagliardi, Laura, Garavelli, Marco, González, Leticia, Guan, Yafu, Guo, Meiyuan, Hennefarth, Matthew R, Hermes, Matthew R, Hoyer, Chad E, Huix-Rotllant, Miquel, Jaiswal, Vishal Kumar, Kaiser, Andy, Kaliakin, Danil S, Khamesian, Marjan, King, Daniel S, Kochetov, Vladislav, Krośnicki, Marek, Kumaar, Arpit Arun, Larsson, Ernst D, Lehtola, Susi, Lepetit, Marie-Bernadette, Lischka, Hans, López Ríos, Pablo, Lundberg, Marcus, Ma, Dongxia, Mai, Sebastian, Marquetand, Philipp, Merritt, Isabella C D, Montorsi, Francesco, Mörchen, Maximilian, Nenov, Artur, Nguyen, Vu Ha Anh, Nishimoto, Yoshio, Oakley, Meagan S, Olivucci, Massimo, Oppel, Markus, Padula, Daniele, Pandharkar, Riddhish, Phung, Quan Manh, Plasser, Felix, Raggi, Gerardo, Rebolini, Elisa, Reiher, Markus, Rivalta, Ivan, Roca-Sanjuán, Daniel, Romig, Thies, Safari, Arta Anushirwan, Sánchez-Mansilla, Aitor, Sand, Andrew M, Schapiro, Igor, Scott, Thais R, Segarra-Martí, Javier, Segatta, Francesco, Sergentu, Dumitru-Claudiu, Sharma, Prachi, Shepard, Ron, Shu, Yinan, Staab, Jakob K, Straatsma, Tjerk P, Sørensen, Lasse Kragh, Tenorio, Bruno Nunes Cabral, Truhlar, Donald G, Ungur, Liviu, Vacher, Morgane, Veryazov, Valera

“… The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible …”
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CRYSTAL23: A Program for Computational Solid State Physics and Chemistry von Erba, Alessandro, Desmarais, Jacques K, Casassa, Silvia, Civalleri, Bartolomeo, Donà, Lorenzo, Bush, Ian J, Searle, Barry, Maschio, Lorenzo, Edith-Daga, Loredana, Cossard, Alessandro, Ribaldone, Chiara, Ascrizzi, Eleonora, Marana, Naiara L, Flament, Jean-Pierre, Kirtman, Bernard

“… The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state …”
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OpenMolcas: From Source Code to Insight von 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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PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges von 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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Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods von 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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OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules von 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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Exploration of chemical compound, conformer, and reaction space with meta-dynamics simulations based on tight-binding quantum chemical calculations von Grimme, Stefan

“… The semi-empirical 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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TURBOMOLE: Today and Tomorrow von Franzke, Yannick J, Holzer, Christof, Andersen, Josefine H, Begušić, Tomislav, Bruder, Florian, Coriani, Sonia, Della Sala, Fabio, Fabiano, Eduardo, Fedotov, Daniil A, Fürst, Susanne, Gillhuber, Sebastian, Grotjahn, Robin, Kaupp, Martin, Kehry, Max, Krstić, Marjan, Mack, Fabian, Majumdar, Sourav, Nguyen, Brian D, Parker, Shane M, Pauly, Fabian, Pausch, Ansgar, Perlt, Eva, Phun, Gabriel S, Rajabi, Ahmadreza, Rappoport, Dmitrij, Samal, Bibek, Schrader, Tim, Sharma, Manas, Tapavicza, Enrico, Treß, Robert S, Voora, Vamsee, Wodyński, Artur, Yu, Jason M, Zerulla, Benedikt, Furche, Filipp, Hättig, Christof, Sierka, Marek, Tew, David P, Weigend, Florian

“… TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and …”
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Bottom-up Coarse-Graining: Principles and Perspectives von Jin, Jaehyeok, Pak, Alexander J, Durumeric, Aleksander E P, Loose, Timothy D, Voth, Gregory A

“… Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior …”
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Scalable Parallel Algorithm for Graph Neural Network Interatomic Potentials in Molecular Dynamics Simulations von Park, Yutack, Kim, Jaesun, Hwang, Seungwoo, Han, Seungwu

“… Message-passing graph neural network interatomic potentials (GNN-IPs), particularly those with equivariant representations such as NequIP, are attracting …”
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Efficient Exploration of Chemical Space with Docking and Deep Learning von Yang, Ying, Yao, Kun, Repasky, Matthew P, Leswing, Karl, Abel, Robert, Shoichet, Brian K, Jerome, Steven V

“… With the advent of make-on-demand commercial libraries, the number of purchasable compounds available for virtual screening and assay has grown explosively in …”
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Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following von Ásgeirsson, Vilhjálmur, Birgisson, Benedikt Orri, Bjornsson, Ragnar, Becker, Ute, Neese, Frank, Riplinger, Christoph, Jónsson, Hannes

“… The climbing image nudged elastic band method (CI-NEB) is used to identify reaction coordinates and to find saddle points representing transition states of …”
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Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens von Devereux, Christian, Smith, Justin S, Davis, Kate K, Barros, Kipton, Zubatyuk, Roman, Isayev, Olexandr, Roitberg, Adrian E

“… Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In …”
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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) von 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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Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability von Parrish, Robert M, Burns, Lori A, Smith, Daniel G A, Simmonett, Andrew C, DePrince, 3rd, 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, 3rd, 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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Generalized Unitary Coupled Cluster Wave functions for Quantum Computation von 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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