Zobrazeno 1 - 10
of 16
pro vyhledávání: '"Ryszard J. Wawak"'
Autor:
Sylwia Rodziewicz-Motowidło, Harold A. Scheraga, Adam Liwo, Daniel R. Ripoll, Cezary Czaplewski, Ryszard J. Wawak
Publikováno v:
International Journal of Quantum Chemistry. 88:41-55
The potential of mean force (PMF) of the hydrophobic association of pairs and triplets of nonpolar solute molecules with various sizes and strengths of van der Waals interactions has been studied by means of umbrella-sampling molecular-dynamic simula
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8be2085dc4d34fbad7b3c3e1ae81cadc
https://doi.org/10.1002/qua.10077
https://doi.org/10.1002/qua.10077
Autor:
Cezary Czaplewski, Kenneth D. Gibson, Jooyoung Lee, Harold A. Scheraga, Ryszard J. Wawak, Adam Liwo, Daniel R. Ripoll, Yelena A. Arnautova, Jaroslaw Pillardy
Publikováno v:
Computer Physics Communications. 128:399-411
Global optimization is playing an increasing role in physics, chemistry, and biophysical chemistry. One of the most important applications of global optimization is to find the global minima of the potential energy of molecules or molecular assemblie
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6128561c5a4b4988b103c1f02b0f64ba
https://doi.org/10.1016/s0010-4655(99)00515-9
https://doi.org/10.1016/s0010-4655(99)00515-9
Autor:
Yelena A. Arnautova, and Cezary Czaplewski, Ryszard J. Wawak, Harold A. Scheraga, Jaroslaw Pillardy
Publikováno v:
Journal of the American Chemical Society. 122:907-921
A recently proposed method for surmounting the multiple-minima problem in protein folding is applied here to the prediction of crystal structures by global optimization of a potential energy function. The method, self-consistent basin-to-deformed-bas
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2514eedff818bcd9dfc8d228f7bcf8bb
https://doi.org/10.1021/ja9929990
https://doi.org/10.1021/ja9929990
Autor:
Stanisaw Ołdziej, Rajmund Kaźmierkiewicz, Małgorzata Groth, Harold A. Scheraga, Ryszard J. Wawak, Adam Liwo, Cezary Czaplewski, Jaroslaw Pillardy
Publikováno v:
Scopus-Elsevier
A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization met
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a50d4121e48e03ae1fca0c90dd62854f
https://doi.org/10.1007/s002140050399
https://doi.org/10.1007/s002140050399
Publikováno v:
The Journal of Physical Chemistry A. 102:2904-2918
Two methods of global minimization, the diffusion equation method and the distance scaling method, are applied to predict the crystal structures of the hexasulfur and benzene molecules. No knowledge about the systems other than the geometry of the mo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::09fe5166d3ca610b97a6d8861818fcc0
https://doi.org/10.1021/jp972424u
https://doi.org/10.1021/jp972424u
Autor:
Matthew R. Pincus, Ryszard J. Wawak, R. Kazmierkiewicz, S. Rackovsky, Harold A. Scheraga, Cezary Czaplewski, Adam Liwo, Stanisław Ołdziej, Małgorzata Groth
Publikováno v:
Journal of Computational Chemistry. 19:259-276
Based on the dipole model of peptide groups developed in our earlier work [Liwo et al., Prot. Sci.,2, 1697 (1993)], a cumulant expansion of the average free energy of the system of freely rotating peptide-group dipoles tethered to a fixed α-carbon t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3c8f1669b99545c7e5c636c2e0cbd548
https://doi.org/10.1002/(sici)1096-987x(199802)19:3<259::aid-jcc1>3.0.co
https://doi.org/10.1002/(sici)1096-987x(199802)19:3<259::aid-jcc1>3.0.co
Autor:
S. Rackovsky, Adam Liwo, Stanisław Ołdziej, Harold A. Scheraga, Ryszard J. Wawak, Matthew R. Pincus
Publikováno v:
Journal of Computational Chemistry. 18:874-887
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7999094620ee789344334cc58d58574f
https://doi.org/10.1002/(sici)1096-987x(199705)18:7<874::aid-jcc2>3.0.co
https://doi.org/10.1002/(sici)1096-987x(199705)18:7<874::aid-jcc2>3.0.co
Autor:
Matthew R. Pincus, Adam Liwo, Stanisław Ołdziej, Harold A. Scheraga, Ryszard J. Wawak, S. Rackovsky
Publikováno v:
Journal of Computational Chemistry. 18:849-873
A two-stage procedure for the determination of a united-residue potential designed for protein simulations is outlined. In the first stage, the long-range and local-interaction energy terms of the total energy of a polypeptide chain are determined by
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::dfeec02228a397d97cacffecdf2394e1
https://doi.org/10.1002/(sici)1096-987x(199705)18:7<849::aid-jcc1>3.0.co
https://doi.org/10.1002/(sici)1096-987x(199705)18:7<849::aid-jcc1>3.0.co
Publikováno v:
Proceedings of the National Academy of Sciences. 93:1743-1746
The diffusion equation method of global minimization is applied to compute the crystal structure of S6, with no a priori knowledge about the system. The experimental lattice parameters and positions and orientations of the molecules in the unit cell
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::579a9721dd4d97a92863112019fb0598
https://doi.org/10.1073/pnas.93.5.1743
https://doi.org/10.1073/pnas.93.5.1743
Publikováno v:
Journal of Mathematical Chemistry. 15:207-232
The free energy of solvation of a polypeptide or a protein can be expressed in terms of the accessible surface area of the molecule. Algorithms for energy minimization or for molecular dynamics, which involve the first derivatives of the energy, incl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4096a259463dcccf32d6bb9aeb57296c
https://doi.org/10.1007/bf01277561
https://doi.org/10.1007/bf01277561