Hits ?▲ |
Authors |
Title |
Venue |
Year |
Link |
Author keywords |
69 | Yaohang Li, Michael Mascagni, Andrey Gorin |
Decentralized Replica Exchange Parallel Tempering: An Efficient Implementation of Parallel Tempering Using MPI and SPRNG. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICCSA (3) ![In: Computational Science and Its Applications - ICCSA 2007, International Conference, Kuala Lumpur, Malaysia, August 26-29, 2007. Proceedings. Part III, pp. 507-519, 2007, Springer, 978-3-540-74482-5. The full citation details ...](Pics/full.jpeg) |
2007 |
DBLP DOI BibTeX RDF |
Parallel Tempering, Parallel Programming, Monte Carlo Methods |
69 | Zhen Li 0010, Manish Parashar |
Grid-based asynchronous replica exchange. ![Search on Bibsonomy](Pics/bibsonomy.png) |
GRID ![In: 8th IEEE/ACM International Conference on Grid Computing (GRID 2007), September 19-21, 2007, Austin, Texas, USA, Proceedings, pp. 201-208, 2007, IEEE Computer Society, 1-4244-1560-8. The full citation details ...](Pics/full.jpeg) |
2007 |
DBLP DOI BibTeX RDF |
|
69 | Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. Pitera, Blake G. Fitch, Ruhong Zhou, Robert S. Germain |
Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L. ![Search on Bibsonomy](Pics/bibsonomy.png) |
IPDPS ![In: 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), Proceedings, 25-29 April 2006, Rhodes Island, Greece, 2006, IEEE. The full citation details ...](Pics/full.jpeg) |
2006 |
DBLP DOI BibTeX RDF |
|
49 | André Luckow, Shantenu Jha, Joohyun Kim 0001, André Merzky, Bettina Schnor |
Distributed Replica-Exchange Simulations on Production Environments Using SAGA and Migol. ![Search on Bibsonomy](Pics/bibsonomy.png) |
eScience ![In: Fourth International Conference on e-Science, e-Science 2008, 7-12 December 2008, Indianapolis, IN, USA, pp. 253-260, 2008, IEEE Computer Society, 978-1-4244-3380-3. The full citation details ...](Pics/full.jpeg) |
2008 |
DBLP DOI BibTeX RDF |
Migol, Replica-Exchange, Fault-Tolerance, Grid Computing, SAGA |
45 | Li Zhang, Manish Parashar, Emilio Gallicchio, Ronald M. Levy |
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICPP ![In: 2006 International Conference on Parallel Processing (ICPP 2006), 14-18 August 2006, Columbus, Ohio, USA, pp. 127-134, 2006, IEEE Computer Society, 0-7695-2636-5. The full citation details ...](Pics/full.jpeg) |
2006 |
DBLP DOI BibTeX RDF |
|
22 | Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita |
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 44(20), pp. 1740-1749, 2023. The full citation details ...](Pics/full.jpeg) |
2023 |
DBLP DOI BibTeX RDF |
|
22 | Christopher Lockhart, Xingyu Luo, Audrey Olson, Bryan M. Delfing, Xavier E. Laracuente, Kenneth W. Foreman, Mikell Paige, Kylene Kehn-Hall, Dmitri K. Klimov |
Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites? ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 63(15), pp. 4791-4802, August 2023. The full citation details ...](Pics/full.jpeg) |
2023 |
DBLP DOI BibTeX RDF |
|
22 | Guang Lin, Christian Moya, Zecheng Zhang |
B-DeepONet: An enhanced Bayesian DeepONet for solving noisy parametric PDEs using accelerated replica exchange SGLD. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Phys. ![In: J. Comput. Phys. 473, pp. 111713, 2023. The full citation details ...](Pics/full.jpeg) |
2023 |
DBLP DOI BibTeX RDF |
|
22 | Guanxun Li, Guang Lin, Zecheng Zhang, Quan Zhou |
Fast Replica Exchange Stochastic Gradient Langevin Dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2301.01898, 2023. The full citation details ...](Pics/full.jpeg) |
2023 |
DBLP DOI BibTeX RDF |
|
22 | Miguel A. Soler, Nikola Minovski, Walter Rocchia, Sara Fortuna |
Replica-exchange optimization of antibody fragments. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Biol. Chem. ![In: Comput. Biol. Chem. 103, pp. 107819, April 2023. The full citation details ...](Pics/full.jpeg) |
2023 |
DBLP DOI BibTeX RDF |
|
22 | Mateusz Marcisz, Margrethe Gaardløs, Krzysztof K. Bojarski, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov |
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 43(24), pp. 1633-1640, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Bryan A. Raubenolt, Steven W. Rick |
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 43(18), pp. 1229-1236, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Daniel Markthaler, Hamzeh Kraus, Niels Hansen |
Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Aided Mol. Des. ![In: J. Comput. Aided Mol. Des. 36(1), pp. 1-9, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Salomé Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emília P. Barros, Philippe H. Hünenberger, Sereina Riniker |
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 62(12), pp. 3043-3056, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Akie Kowaguchi, Katsuhiro Endo, Paul E. Brumby, Kentaro Nomura, Kenji Yasuoka |
Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 62(24), pp. 6544-6552, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Guang Lin, Yating Wang, Zecheng Zhang |
Multi-variance replica exchange SGMCMC for inverse and forward problems via Bayesian PINN. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Phys. ![In: J. Comput. Phys. 460, pp. 111173, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Na Ou, Zecheng Zhang, Guang Lin |
A replica exchange preconditioned Crank-Nicolson Langevin dynamic MCMC method for Bayesian inverse problems. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2210.17048, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Hiroaki Inoue, Koji Hukushima, Toshiaki Omori |
Estimating Distributions of Parameters in Nonlinear State Space Models with Replica Exchange Particle Marginal Metropolis-Hastings Method. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Entropy ![In: Entropy 24(1), pp. 115, 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Ameya Harmalkar, Sai Pooja Mahajan, Jeffrey J. Gray |
Induced fit with replica exchange improves protein complex structure prediction. ![Search on Bibsonomy](Pics/bibsonomy.png) |
PLoS Comput. Biol. ![In: PLoS Comput. Biol. 18(6), 2022. The full citation details ...](Pics/full.jpeg) |
2022 |
DBLP DOI BibTeX RDF |
|
22 | Arthur Voronin |
Application and Optimization of Contact-Guided Replica Exchange Molecular Dynamics ![Search on Bibsonomy](Pics/bibsonomy.png) |
|
2022 |
RDF |
|
22 | Chudong Xu, Shengdong Lu, Yongfeng Kong, Wanjie Xiong |
The enhanced sampling in parallel finite-time dynamics method with replica exchange. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 263, pp. 107911, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Jing Dong, Xin T. Tong |
Replica Exchange for Non-Convex Optimization. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Mach. Learn. Res. ![In: J. Mach. Learn. Res. 22, pp. 173:1-173:59, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP BibTeX RDF |
|
22 | Martyna Maszota-Zieleniak, Mateusz Marcisz, Malgorzata M. Kogut, Till Siebenmorgen, Martin Zacharias, Sergey A. Samsonov |
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 42(15), pp. 1040-1053, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Anji Babu Kapakayala, Nisanth N. Nair |
Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 42(31), pp. 2233-2240, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Anupam Banerjee, Kuntal Pal, Pralay Mitra |
An Evolutionary Profile Guided Greedy Parallel Replica-Exchange Monte Carlo Search Algorithm for Rapid Convergence in Protein Design. ![Search on Bibsonomy](Pics/bibsonomy.png) |
IEEE ACM Trans. Comput. Biol. Bioinform. ![In: IEEE ACM Trans. Comput. Biol. Bioinform. 18(2), pp. 489-499, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Mahdi Ghorbani, Phillip S. Hudson, Michael R. Jones, Félix Aviat, Rubén Meana-Pañeda, Jeffery B. Klauda, Bernard R. Brooks |
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Aided Mol. Des. ![In: J. Comput. Aided Mol. Des. 35(5), pp. 667-677, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Steven W. Rick, Gregory J. Schwing, Christopher M. Summa |
An Implementation of Replica Exchange with Dynamical Scaling for Efficient Large-Scale Simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 61(2), pp. 810-818, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Karnesh Jain, Othman Ghribi, Jerome Delhommelle |
Folding Free-Energy Landscape of α-Synuclein (35-97) Via Replica Exchange Molecular Dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 61(1), pp. 432-443, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Arthur Voronin, Alexander Schug |
pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Open Source Softw. ![In: J. Open Source Softw. 6(68), pp. 3325, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski |
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Bioinform. ![In: Bioinform. 37(11), pp. 1613-1615, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP DOI BibTeX RDF |
|
22 | Guang Lin, Christian Moya, Zecheng Zhang |
Accelerated replica exchange stochastic gradient Langevin diffusion enhanced Bayesian DeepONet for solving noisy parametric PDEs. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2111.02484, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP BibTeX RDF |
|
22 | Guang Lin, Yating Wang, Zecheng Zhang |
Multi-variance replica exchange stochastic gradient MCMC for inverse and forward Bayesian physics-informed neural network. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2107.06330, 2021. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP BibTeX RDF |
|
22 | Wei Deng 0002, Qi Feng 0005, Georgios Karagiannis, Guang Lin, Faming Liang |
Accelerating Convergence of Replica Exchange Stochastic Gradient MCMC via Variance Reduction. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICLR ![In: 9th International Conference on Learning Representations, ICLR 2021, Virtual Event, Austria, May 3-7, 2021, 2021, OpenReview.net. The full citation details ...](Pics/full.jpeg) |
2021 |
DBLP BibTeX RDF |
|
22 | Till Siebenmorgen, Michael Engelhard, Martin Zacharias |
Prediction of protein-protein complexes using replica exchange with repulsive scaling. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 41(15), pp. 1436-1447, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP DOI BibTeX RDF |
|
22 | Till Siebenmorgen, Martin Zacharias |
Efficient Refinement and Free Energy Scoring of Predicted Protein-Protein Complexes Using Replica Exchange with Repulsive Scaling. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 60(11), pp. 5552-5562, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP DOI BibTeX RDF |
|
22 | Keivan Dabiri, Mehrdad Malekmohammadi, Ali Sheikholeslami, Hirotaka Tamura |
Replica Exchange MCMC Hardware With Automatic Temperature Selection and Parallel Trial. ![Search on Bibsonomy](Pics/bibsonomy.png) |
IEEE Trans. Parallel Distributed Syst. ![In: IEEE Trans. Parallel Distributed Syst. 31(7), pp. 1681-1692, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP DOI BibTeX RDF |
|
22 | Yi Chen, Jinglin Chen, Jing Dong 0007, Jian Peng 0001, Zhaoran Wang 0001 |
Accelerating Nonconvex Learning via Replica Exchange Langevin Diffusion. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2007.01990, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP BibTeX RDF |
|
22 | Wei Deng 0002, Qi Feng 0005, Georgios Karagiannis, Guang Lin, Faming Liang |
Accelerating Convergence of Replica Exchange Stochastic Gradient MCMC via Variance Reduction. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2010.01084, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP BibTeX RDF |
|
22 | Wei Deng 0002, Qi Feng 0005, Liyao Gao, Faming Liang, Guang Lin |
Non-convex Learning via Replica Exchange Stochastic Gradient MCMC. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/2008.05367, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP BibTeX RDF |
|
22 | Wenyi Zhang 0003, Eric W. Bell, Minghao Yin, Yang Zhang 0040 |
EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Cheminformatics ![In: J. Cheminformatics 12(1), pp. 37, 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP DOI BibTeX RDF |
|
22 | Rui Luo 0001, Qiang Zhang, Yaodong Yang 0001, Jun Wang 0012 |
Replica-Exchange Nosé-Hoover Dynamics for Bayesian Learning on Large Datasets. ![Search on Bibsonomy](Pics/bibsonomy.png) |
NeurIPS ![In: Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, NeurIPS 2020, December 6-12, 2020, virtual., 2020. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP BibTeX RDF |
|
22 | Wei Deng 0002, Qi Feng 0005, Liyao Gao, Faming Liang, Guang Lin |
Non-convex Learning via Replica Exchange Stochastic Gradient MCMC. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICML ![In: Proceedings of the 37th International Conference on Machine Learning, ICML 2020, 13-18 July 2020, Virtual Event., pp. 2474-2483, 2020, PMLR. The full citation details ...](Pics/full.jpeg) |
2020 |
DBLP BibTeX RDF |
|
22 | Junchao Xia, William F. Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson, Ronald M. Levy |
Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 59(4), pp. 1382-1397, 2019. The full citation details ...](Pics/full.jpeg) |
2019 |
DBLP DOI BibTeX RDF |
|
22 | Rui Luo 0001, Qiang Zhang, Yaodong Yang 0001, Jun Wang 0012 |
Replica-exchange Nosé-Hoover dynamics for Bayesian learning on large datasets. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/1905.12569, 2019. The full citation details ...](Pics/full.jpeg) |
2019 |
DBLP BibTeX RDF |
|
22 | Wangdong Deng, Shotaro Kamiya, Koji Yamamoto 0001, Takayuki Nishio, Masahiro Morikura |
Replica Exchange Spatial Adaptive Play for Channel Allocation in Cognitive Radio Networks. ![Search on Bibsonomy](Pics/bibsonomy.png) |
VTC Spring ![In: 89th IEEE Vehicular Technology Conference, VTC Spring 2019, Kuala Lumpur, Malaysia, April 28 - May 1, 2019, pp. 1-5, 2019, IEEE, 978-1-7281-1217-6. The full citation details ...](Pics/full.jpeg) |
2019 |
DBLP DOI BibTeX RDF |
|
22 | Yi Chen, Jinglin Chen, Jing Dong 0007, Jian Peng 0001, Zhaoran Wang 0001 |
Accelerating Nonconvex Learning via Replica Exchange Langevin diffusion. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICLR (Poster) ![In: 7th International Conference on Learning Representations, ICLR 2019, New Orleans, LA, USA, May 6-9, 2019, 2019, OpenReview.net. The full citation details ...](Pics/full.jpeg) |
2019 |
DBLP BibTeX RDF |
|
22 | Attila Laszlo Boer |
Implementation of the replica-exchange Wang-Landau sampling on Graphics Processing Units (GPUs). ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 233, pp. 62-66, 2018. The full citation details ...](Pics/full.jpeg) |
2018 |
DBLP DOI BibTeX RDF |
|
22 | Shingo Ito, Dmitri G. Fedorov, Yuko Okamoto, Stephan Irle |
Implementation of replica-exchange umbrella sampling in GAMESS. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 228, pp. 152-162, 2018. The full citation details ...](Pics/full.jpeg) |
2018 |
DBLP DOI BibTeX RDF |
|
22 | Richard Platania, Shayan Shams, Chui-Hui Chiu, Nayong Kim, Joohyun Kim 0001, Seung-Jong Park |
Hadoop-based replica exchange over heterogeneous distributed cyberinfrastructures. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Concurr. Comput. Pract. Exp. ![In: Concurr. Comput. Pract. Exp. 29(4), 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Kuo-Hao Lee, Jianhan Chen |
Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 38(30), pp. 2632-2640, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee 0002, Adam Liwo |
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 38(31), pp. 2730-2746, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Mark A. Olson, Michael S. Lee, In-Chul Yeh |
Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 38(16), pp. 1342-1352, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Michio Iwaoka, Toshiki Suzuki, Yuya Shoji, Kenichi Dedachi, Taku Shimosato, Toshiya Minezaki, Hironobu Hojo, Hiroyuki Onuki, Hiroshi Hirota |
Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Aided Mol. Des. ![In: J. Comput. Aided Mol. Des. 31(12), pp. 1039-1052, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Hongrui Wang, Hongwei Liu, Leixin Cai, Caixia Wang, Qiang Lv |
Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking. ![Search on Bibsonomy](Pics/bibsonomy.png) |
BMC Bioinform. ![In: BMC Bioinform. 18(1), pp. 327, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Wasinee Khuntawee, Manaschai Kunaseth, Chompoonut Rungnim, Suradej Intagorn, Peter Wolschann, Nawee Kungwan, Thanyada Rungrotmongkol, Supot Hannongbua |
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 57(4), pp. 778-786, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Zhangwei Li, Xiaohu Hao, Guijun Zhang |
基于副本交换的局部增强差分进化蛋白质结构从头预测方法 (Replica Exchange Based Local Enhanced Differential Evolution Searching Method in Ab-initio Protein Structure Prediction). ![Search on Bibsonomy](Pics/bibsonomy.png) |
计算机科学 ![In: 计算机科学 44(5), pp. 211-217, 2017. The full citation details ...](Pics/full.jpeg) |
2017 |
DBLP DOI BibTeX RDF |
|
22 | Shingo Ito, Stephan Irle, Yuko Okamoto |
Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 204, pp. 1-10, 2016. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
|
22 | David Mignon, Thomas Simonson |
Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 37(19), pp. 1781-1793, 2016. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
|
22 | Changjun Chen, Yanzhao Huang |
Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 37(17), pp. 1565-1575, 2016. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
|
22 | Pongsakorn Kanjanatanin, Rath Pichyangkura, Surasak Chunsrivirot |
Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths. ![Search on Bibsonomy](Pics/bibsonomy.png) |
BMC Bioinform. ![In: BMC Bioinform. 17, pp. 306, 2016. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
|
22 | Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha |
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/1601.05439, 2016. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP BibTeX RDF |
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22 | Teng Liu, Qingzhong Li, Lanju Kong, Lei Liu 0003, Li-zhen Cui |
Optimizing Replica Exchange Strategy for Load Balancing in Multienant Databases. ![Search on Bibsonomy](Pics/bibsonomy.png) |
WAIM (2) ![In: Web-Age Information Management - 17th International Conference, WAIM 2016, Nanchang, China, June 3-5, 2016, Proceedings, Part II, pp. 430-443, 2016, Springer, 978-3-319-39957-7. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
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22 | Antons Treikalis, André Merzky, Haoyuan Chen, Tai-Sung Lee, Darrin M. York, Shantenu Jha |
RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
ICPP ![In: 45th International Conference on Parallel Processing, ICPP 2016, Philadelphia, PA, USA, August 16-19, 2016, pp. 628-637, 2016, IEEE Computer Society, 978-1-5090-2823-8. The full citation details ...](Pics/full.jpeg) |
2016 |
DBLP DOI BibTeX RDF |
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22 | Emilio Gallicchio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes, Ronald M. Levy |
Asynchronous replica exchange software for grid and heterogeneous computing. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 196, pp. 236-246, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Ryo Urano, Yuko Okamoto |
Designed-walk replica-exchange method for simulations of complex systems. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 196, pp. 380-383, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Liang-Chun Liu, Jer-Lai Kuo |
A LAMMPS implementation of volume-temperature replica exchange molecular dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 189, pp. 119-127, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Sunhwan Jo, Wei Jiang |
A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 197, pp. 304-311, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Ryo Urano, Yuko Okamoto |
Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 197, pp. 128-135, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan, Ronald M. Levy |
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 36(23), pp. 1772-1785, 2015. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Nayong Kim, Richard Platania, Wei Huang, Chris Knight 0001, Tom Keyes, Seung-Jong Park, Joohyun Kim 0001 |
Enabling Large-Scale Biomolecular Conformation Search with Replica Exchange Statistical Temperature Molecular Dynamics (RESTMD) over HPC and Cloud Computing Resources. ![Search on Bibsonomy](Pics/bibsonomy.png) |
AINA Workshops ![In: 29th IEEE International Conference on Advanced Information Networking and Applications Workshops, AINA 2015 Workshops, Gwangju, South Korea, March 24-27, 2015, pp. 61-66, 2015, IEEE Computer Society, 978-1-4799-1775-4. The full citation details ...](Pics/full.jpeg) |
2015 |
DBLP DOI BibTeX RDF |
|
22 | Weihong Zhang, Jianhan Chen |
Replica exchange with guided annealing for accelerated sampling of disordered protein conformations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 35(23), pp. 1682-1689, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Katja Ostermeir, Martin Zacharias |
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 35(2), pp. 150-158, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Hsin-Lin Chiang, Chun-Jung Chen, Hisashi Okumura, Chin-Kun Hu |
Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 35(19), pp. 1430-1437, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita |
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 35(4), pp. 300-308, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Manuel P. Luitz, Martin Zacharias |
Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Chem. Inf. Model. ![In: J. Chem. Inf. Model. 54(6), pp. 1669-1675, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Cameron Abrams, Giovanni Bussi |
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Entropy ![In: Entropy 16(1), pp. 163-199, 2014. The full citation details ...](Pics/full.jpeg) |
2014 |
DBLP DOI BibTeX RDF |
|
22 | Mark A. Olson, Michael S. Lee |
Application of replica exchange umbrella sampling to protein structure refinement of nontemplate models. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 34(20), pp. 1785-1793, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | Yannick G. Spill, Guillaume Bouvier, Michael Nilges |
A convective replica-exchange method for sampling new energy basins. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 34(2), pp. 132-140, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | Satoru G. Itoh, Hisashi Okumura |
Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 34(8), pp. 622-639, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | Yannick G. Spill, Guillaume Bouvier, Michael Nilges |
Erratum: A convective replica-exchange method for sampling new energy basins. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 34(18), pp. 1609, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
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22 | Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto |
Two-dimensional replica-exchange method for predicting protein-ligand binding structures. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 34(30), pp. 2601-2614, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
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22 | Kai Wang, John D. Chodera, Yanzhi Yang, Michael R. Shirts |
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Aided Mol. Des. ![In: J. Comput. Aided Mol. Des. 27(12), pp. 989-1007, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | Hiqmet Kamberaj |
Replica Exchange using q-Gaussian Swarm Quantum Particle Intelligence Method. ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/1312.7326, 2013. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP BibTeX RDF |
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22 | Brian K. Radak, Tai-Sung Lee, Peng He, Melissa Romanus, Ole Weidner, Wei Dai, Emilio Gallicchio, Nan-Jie Deng, Darrin M. York, Ronald M. Levy, Shantenu Jha |
A framework for flexible and scalable replica-exchange on production distributed CI. ![Search on Bibsonomy](Pics/bibsonomy.png) |
XSEDE ![In: Extreme Science and Engineering Discovery Environment: Gateway to Discovery, XSEDE13, San Diego, CA, USA - July 22 - 25, 2013, pp. 26:1-26:8, 2013, ACM, 978-1-4503-2170-9. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
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22 | Maritza Smith-Romero, Jin Niu, Alvin Allen, Abrahim Khosravi, Shuju Bai |
Implementing replica exchange molecular dynamics using work queue. ![Search on Bibsonomy](Pics/bibsonomy.png) |
BIBM ![In: 2013 IEEE International Conference on Bioinformatics and Biomedicine, Shanghai, China, December 18-21, 2013, pp. 63-64, 2013, IEEE Computer Society, 978-1-4799-1309-1. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | Hisanari Otsu, Yonghao Yue, Qiming Hou, Kei Iwasaki, Yoshinori Dobashi, Tomoyuki Nishita |
Replica exchange light transport on relaxed distributions. ![Search on Bibsonomy](Pics/bibsonomy.png) |
SIGGRAPH Posters ![In: Special Interest Group on Computer Graphics and Interactive Techniques Conference, SIGGRAPH '13, Anaheim, CA, USA, July 21-25, 2013, Poster Proceedings, pp. 106, 2013, ACM, 978-1-4503-2342-0. The full citation details ...](Pics/full.jpeg) |
2013 |
DBLP DOI BibTeX RDF |
|
22 | H.-H. Wu, C.-C. Chen, Chi-Ming Chen |
Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Aided Mol. Des. ![In: J. Comput. Aided Mol. Des. 26(3), pp. 363-374, 2012. The full citation details ...](Pics/full.jpeg) |
2012 |
DBLP DOI BibTeX RDF |
|
22 | Jonathan Gross, Wolfhard Janke, Michael Bachmann |
Massively parallelized replica-exchange simulations of polymers on GPUs. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 182(8), pp. 1638-1644, 2011. The full citation details ...](Pics/full.jpeg) |
2011 |
DBLP DOI BibTeX RDF |
|
22 | Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto |
Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 32(13), pp. 2810-2821, 2011. The full citation details ...](Pics/full.jpeg) |
2011 |
DBLP DOI BibTeX RDF |
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22 | Tsuyoshi Terakawa, Tomoshi Kameda, Shoji Takada |
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 32(7), pp. 1228-1234, 2011. The full citation details ...](Pics/full.jpeg) |
2011 |
DBLP DOI BibTeX RDF |
|
22 | Srinivasaraghavan Kannan, Wolfgang Sippl, Martin Zacharias |
Application of biasing-potential replica exchange simulations for loop modeling and refinement of proteins in explicit solvent. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Cheminformatics ![In: J. Cheminformatics 3(S-1), pp. 33, 2011. The full citation details ...](Pics/full.jpeg) |
2011 |
DBLP DOI BibTeX RDF |
|
22 | Hisashi Okumura, Emilio Gallicchio, Ronald M. Levy |
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 31(7), pp. 1357-1367, 2010. The full citation details ...](Pics/full.jpeg) |
2010 |
DBLP DOI BibTeX RDF |
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22 | Jory Z. Ruscio, Nicolas L. Fawzi, Teresa Head-Gordon |
How hot? Systematic convergence of the replica exchange method using multiple reservoirs. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 31(3), pp. 620-627, 2010. The full citation details ...](Pics/full.jpeg) |
2010 |
DBLP DOI BibTeX RDF |
|
22 | Leonidas Kapsokalivas, Kathleen Steinhöfel |
A Replica Exchange Monte Carlo Algorithm for the Optimization of Secondary Structure Packing in Proteins. ![Search on Bibsonomy](Pics/bibsonomy.png) |
EvoBIO ![In: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 8th European Conference, EvoBIO 2010, Istanbul, Turkey, April 7-9, 2010. Proceedings, pp. 146-157, 2010, Springer, 978-3-642-12210-1. The full citation details ...](Pics/full.jpeg) |
2010 |
DBLP DOI BibTeX RDF |
|
22 | Evgeni S. Penev, Sotiria Lampoudi, Joan-Emma Shea |
TiReX: Replica-exchange molecular dynamics using Tinker. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Phys. Commun. ![In: Comput. Phys. Commun. 180(10), pp. 2013-2019, 2009. The full citation details ...](Pics/full.jpeg) |
2009 |
DBLP DOI BibTeX RDF |
|
22 | Mikolai Fajer, Robert V. Swift, James Andrew McCammon |
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 30(11), pp. 1719-1725, 2009. The full citation details ...](Pics/full.jpeg) |
2009 |
DBLP DOI BibTeX RDF |
|
22 | Shinya Kitaoka, Yoshifumi Kitamura, Fumio Kishino |
Replica Exchange Light Transport. ![Search on Bibsonomy](Pics/bibsonomy.png) |
Comput. Graph. Forum ![In: Comput. Graph. Forum 28(8), pp. 2330-2342, 2009. The full citation details ...](Pics/full.jpeg) |
2009 |
DBLP DOI BibTeX RDF |
|
22 | Emilio Gallicchio, Ronald M. Levy, Manish Parashar |
Asynchronous replica exchange for molecular simulations. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 29(5), pp. 788-794, 2008. The full citation details ...](Pics/full.jpeg) |
2008 |
DBLP DOI BibTeX RDF |
|
22 | Giovanni Bussi |
A simple asynchronous replica-exchange implementation ![Search on Bibsonomy](Pics/bibsonomy.png) |
CoRR ![In: CoRR abs/0812.1633, 2008. The full citation details ...](Pics/full.jpeg) |
2008 |
DBLP BibTeX RDF |
|
22 | José D. Faraldo-Gómez, Benoît Roux |
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. ![Search on Bibsonomy](Pics/bibsonomy.png) |
J. Comput. Chem. ![In: J. Comput. Chem. 28(10), pp. 1634-1647, 2007. The full citation details ...](Pics/full.jpeg) |
2007 |
DBLP DOI BibTeX RDF |
|