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 41 to 60 of 120.
Sorted by year (citations)
  1. Frausto-Solís, Juan; Sánchez-Pérez, Mishael; Lińan-García, Ernesto; Sánchez-Hernández, Juan Paulo: Threshold temperature tuning simulated annealing for protein folding problem in small peptides (2013) ioport
  2. Harris, Robert C.; Mackoy, Travis; Fenley, Marcia O.: A stochastic solver of the generalized Born model (2013)
  3. Kreienkamp, Amelia B.; Liu, Lucy Y.; Minkara, Mona S.; Knepley, Matthew G.; Bardhan, Jaydeep P.; Radhakrishnan, Mala L.: Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding (2013)
  4. Li, Chuan; Li, Lin; Petukh, Marharyta; Alexov, Emil: Progress in developing Poisson-Boltzmann equation solvers (2013)
  5. Lu, Benzhuo: Finite element modeling of biomolecular systems in ionic solution (2013)
  6. Oden, J. Tinsley; Prudencio, Ernesto E.; Bauman, Paul T.: Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics (2013)
  7. Park, Jun-Koo; Jernigan, Robert; Wu, Zhijun: Coarse grained normal mode analysis vs. refined Gaussian network model for protein residue-level structural fluctuations (2013)
  8. Ryu, Joonghyun; Kim, Deok-Soo: Protein structure optimization by side-chain positioning via beta-complex (2013)
  9. Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil: DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes (2013)
  10. Scherer, Philipp O. J.: Computational physics. Simulation of classical and quantum systems (2013)
  11. Vedell, Peter; Wu, Zhijun: The solution of the boundary-value problems for the simulation of transition of protein conformation (2013)
  12. Votapka, Lane W.; Czapla, Luke; Zhenirovskyy, Maxim; Amaro, Rommie E.: DelEnsembleElec: computing ensemble-averaged electrostatics using DelPhi (2013)
  13. Xiang, Ping; Liew, K. M.: A computational framework for transverse compression of microtubules based on a higher-order Cauchy-Born rule (2013)
  14. Aksoylu, Burak; Bond, Stephen D.; Cyr, Eric C.; Holst, Michael: Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation (2012)
  15. Heinke, Florian; Labudde, Dirk: Membrane protein stability analyses by means of protein energy profiles in case of nephrogenic diabetes insipidus (2012)
  16. Lilkova, Elena; Nacheva, Genoveva; Petkov, Peicho; Petkov, Petko; Markov, Stoyan; Ilieva, Nevena; Litov, Leandar: Metadynamics study of mutant human interferon-gamma forms (2012)
  17. Lima, Angélica Nakagawa; Philot, Eric Allison; Perahia, David; Braz, Antonio Sérgio Kimus; Scott, Luis P. B.: GANM: A protein-ligand docking approach based on genetic algorithm and normal modes (2012)
  18. Qin, Zhao; Buehler, Markus J.: Computational and theoretical modeling of intermediate filament networks: structure, mechanics and disease (2012)
  19. Yaseen, Ashraf; Li, Yaohang: Accelerating knowledge-based energy evaluation in protein structure modeling with graphics processing units (2012) ioport
  20. Zhang, Zhe; Miteva, Maria A.; Wang, Lin; Alexov, Emil: Analyzing effects of naturally occurring missense mutations (2012)

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