CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM models the dynamics and mechanics of macromolecular systems using empirical and mixed empirical/quantum mechanical force fields. CHARMM is designed to investigate the structure and dynamics of large molecules. It performs free energy calculations of mutations and drug binding as well as conformational folding of peptides. It uses classical mechanical methods to investigate potential energy surfaces derived from experimental and ”ab initio” quantum chemical calculations. In addition, mixed quantum mechanical/classical systems can be defined to investigate chemical processes such as enzyme catalysis.


References in zbMATH (referenced in 120 articles )

Showing results 21 to 40 of 120.
Sorted by year (citations)
  1. Friedrich, Manuel; Piovano, Paolo; Stefanelli, Ulisse: The geometry of (C_60): a rigorous approach via molecular mechanics (2016)
  2. Gebbie-Rayet, J., Shannon, G., Loeffler, H.H., Laughton, C.A.: Longbow: A Lightweight Remote Job Submission Tool (2016) not zbMATH
  3. Gogolinska, Anna; Jakubowski, Rafal; Nowak, Wieslaw: Petri nets formalism facilitates analysis of complex biomolecular structural data (2016)
  4. Mishra, Avdesh; Iqbal, Sumaiya; Hoque, Md Tamjidul: Discriminate protein decoys from native by using a scoring function based on ubiquitous phi and psi angles computed for all atom (2016)
  5. Sun, Kwang Woong; Ambrosia, Matthew Stanley; Kwon, Tae Woo; Ha, Man Yeong: A hydrophobicity study on wavy and orthogonal textured surfaces (2016)
  6. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  7. Cang, Zixuan; Mu, Lin; Wu, Kedi; Opron, Kristopher; Xia, Kelin; Wei, Guo-Wei: A topological approach for protein classification (2015)
  8. Cisneros-Ake, Luis A.; Cruzeiro, Leonor; Velarde, Manuel G.: Mobile localized solutions for an electron in lattices with dispersive and non-dispersive phonons (2015)
  9. Farrell, Kathryn; Oden, J. Tinsley; Faghihi, Danial: A Bayesian framework for adaptive selection, calibration, and validation of coarse-grained models of atomistic systems (2015)
  10. Ko, Jeong-Ahn; Ambrosia, Matthew; Ha, Man Yeong: A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces (2015)
  11. Lampariello, Francesco; Liuzzi, Giampaolo: Global optimization of protein-peptide docking by a filling function method (2015)
  12. Leimkuhler, Ben; Matthews, Charles: Molecular dynamics. With deterministic and stochastic numerical methods (2015)
  13. Mark James Abraham; Teemu Murtola; Roland Schulz; Szilárd Páll; Jeremy C.Smith; Berk Hess; Erik Lindahl: GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers (2015) not zbMATH
  14. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  15. Chen, Duan: Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules (2014)
  16. Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Song, Chanyoung; Kim, Deok-Soo: BetaSCP2: a program for the optimal prediction of side-chains in proteins (2014)
  17. Xia, Kelin; Wei, Guo-Wei: Molecular nonlinear dynamics and protein thermal uncertainty quantification (2014)
  18. Xie, Dexuan: New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics (2014)
  19. Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Zhi-Qin; Anh, Vo: Fractal and complex network analyses of protein molecular dynamics (2014)
  20. Almeida, Fabio C. L.; Moraes, Adolfo H.; Gomes-Neto, Francisco A. M.: An overview on protein structure determination by NMR: historical and future perspectives of the use of distance geometry methods (2013)

Further publications can be found at: http://www.charmm.org/info/literature.html