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 81 to 100 of 120.
Sorted by year (citations)
  1. Cai, Wei; Xu, Zhenli; Baumketner, Andrij: A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation (2008)
  2. Jiang, Hanqing; Jiang, Liying; Posner, Jonathan D.; Vogt, Bryan D.: Atomistic-based continuum constitutive relation for microtubules: elastic modulus prediction (2008)
  3. Anderson, Kurt; Mukherjee, Rudranarayan; Critchley, James; Ziegler, John; Lipton, Scott: POEMS: parallelizable open-source efficient multibody software (2007) ioport
  4. Anile, A. M.; Cutello, V.; Narzisi, G.; Nicosia, G.; Spinella, S.: Determination of protein structure and dynamics combining immune algorithms and pattern search methods (2007)
  5. Iii, H. Lee Woodcock; Hodoscek, Milan; Gilbert, Andrew T. B.; Gill, Peter M. W.; Iii, Henry F. Schaefer; Brooks, Bernard R.: Interfacing q-chem and CHARMM to perform QM/MM reaction path calculations. (2007) ioport
  6. Lavor, Carlile: Analytic evaluation of the gradient and Hessian of molecular potential energy functions (2007)
  7. Mordvitsev, D. Yu.; Polyak, Ya. L.; Kuzmin, D. A.; Levtsova, O. V.; Tourleigh, Ye. V.; Utkin, Yu. N.; Shaitan, K. V.; Tsetlin, V. I.: Computer modeling of binding of diverse weak toxins to nicotinic acetylcholine receptors (2007)
  8. Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko: Long-range interactions and parallel scalability in molecular simulations (2007) ioport
  9. Barth, Eric; Leimkuhler, Ben; Sweet, Chris: Approach to thermal equilibrium in biomolecular simulation (2006)
  10. Crommelin, D. T.; Vanden-Eijnden, E.: Fitting timeseries by continuous-time Markov chains: a quadratic programming approach (2006)
  11. Gunther, Stefan; Senger, Christian; Michalsky, Elke; Goede, Andrean; Preissner, Robert: Representation of target-bound drugs by computed conformers: Implications for conformational libraries (2006) ioport
  12. Li, Aiqin; Dowell, Earl H.: Modal reduction of mathematical models of biological molecules (2006)
  13. Liu, L. Angela; Bader, Joel S.: Decoding transcriptional regulatory interactions (2006)
  14. Patel, Sandeep; Brooks, Charles L.: Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems (2006)
  15. Tang, Deman; Attar, Peter; Li, Aiqin; Dowell, Earl H.: Complex dynamics of a pyranose ring structure molecule attached to an atomic force microscope (2006)
  16. Shi, Xinghua; Kong, Yong; Zhao, Yapu; Gao, Huajian: Molecular dynamics simulation of peeling a DNA molecule on substrate (2005)
  17. Tuszyński, J. A.; Brown, J. A.; Crawford, E.; Carpenter, E. J.; Nip, M. L. A.; Dixon, J. M.; Satarić, M. V.: Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules (2005)
  18. Vaiana, A. C.; Cournia, Z.; Costescu, I. B.; Smith, J. C.: AFMM: A molecular mechanics force field vibrational parametrization program (2005) ioport
  19. Eskow, Elizabeth; Bader, Brett; Byrd, Richard; Crivelli, Silvia; Head-Gordon, Teresa; Lamberti, Vincent; Schnabel, Robert: An optimization approach to the problem of protein structure prediction (2004)
  20. Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles: Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS (2004)

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