Zobrazeno 1 - 10
of 21
pro vyhledávání: '"M. Chinchio"'
Publikováno v:
Journal of chemical theory and computation. 3(4)
Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds in the context of protein structure prediction, but none can si
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79ee227def5c4067607aecf74dd4e23a
https://pubmed.ncbi.nlm.nih.gov/26633198
https://pubmed.ncbi.nlm.nih.gov/26633198
Publikováno v:
Multiscale Modeling & Simulation. 5:1175-1195
A hierarchical, two‐stage approach to ab initio protein structure prediction is presented and applied to four α‐helical proteins. In the first stage, a bank of low‐resolution models is generated using a highly simplified protein representation
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::8168eaa9707712f151b63a23517fa721
https://doi.org/10.1137/060649318
https://doi.org/10.1137/060649318
Autor:
Cezary Czaplewski, Stanisław Ołdziej, M. Chinchio, Mariusz Makowski, Jeffrey A. Saunders, Harold A. Scheraga, H. D. Schafroth, Adam Liwo, Daniel R. Ripoll, Mey Khalili, Yelena A. Arnautova, Marian Nanias, Jorge A. Vila, Kenneth D. Gibson, Rajmund Kaźmierkiewicz, Young Kee Kang, Jaroslaw Pillardy, A. Jagielska
Publikováno v:
Proceedings of the National Academy of Sciences. 102:7547-7552
Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::474521e9446f2647370b3de0809c35f5
https://doi.org/10.1073/pnas.0502655102
https://doi.org/10.1073/pnas.0502655102
Publikováno v:
Journal of Computational Chemistry. 26:1472-1486
Two current methods of global optimization are coupled to produce the Replica-Exchange method together with Monte Carlo-with-Minimization (REMCM). Its performance is compared with each separate component and with other global optimization techniques.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3b9227a34876b4c3a47adb1e1bbeeb8
https://doi.org/10.1002/jcc.20286
https://doi.org/10.1002/jcc.20286
Autor:
Cezary Czaplewski, Adam Liwo, Harold A. Scheraga, and Marian Nanias, Stanisław Ołdziej, M. Chinchio, Justyna Ła̧giewka
Publikováno v:
The Journal of Physical Chemistry B. 108:16950-16959
We report the application of the hierarchical optimization method of protein potential-energy landscapes described in the accompanying papers (Liwo, A.; Arlukowicz, P.; Oldziej, S.; Czaplewski, C.;...
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9adb0109965c311e300da108d02b0751
https://doi.org/10.1021/jp040329x
https://doi.org/10.1021/jp040329x
Publikováno v:
Proceedings of the National Academy of Sciences. 100:1706-1710
An efficient method has been developed for packing α-helices in proteins. It treats α-helices as rigid bodies and uses a simplified Lennard–Jones potential with Miyazawa–Jernigan contact-energy parameters to describe the interactions between th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dd9df463c5b16c9e7d0493e53aa0c49d
https://doi.org/10.1073/pnas.252760199
https://doi.org/10.1073/pnas.252760199
Autor:
Young Kee Kang, Mey Khalili, Cezary Czaplewski, Marian Nanias, Jorge A. Vila, Stanisław Ołdziej, Ron Elber, Jeffrey A. Saunders, Jooyoung Lee, Avijit Ghosh, A. Jagielska, Adam Liwo, Daniel R. Ripoll, Jaroslaw Pillardy, M. Chinchio, H. D. Schafroth, Harold A. Scheraga, Kenneth D. Gibson, R. Kazmierkiewicz, Mariusz Makowski, Yelena A. Arnautova
Publikováno v:
New Algorithms for Macromolecular Simulation ISBN: 3540255427
The two types of protein folding problems (theoretical predictions of protein structure and folding pathways) are discussed. Most of the effort in our laboratory has been devoted to computing three-dimensional structures of proteins from amino acid s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4156ed3a4066cb314219d9128544f0f6
https://doi.org/10.1007/3-540-31618-3_6
https://doi.org/10.1007/3-540-31618-3_6
Autor:
A. Jagielska, M. Chinchio, Harold A. Scheraga, Jeffrey A. Saunders, Yelena A. Arnautova, R. Kazmierkiewicz, Marian Nanias, Jorge A. Vila, S. Oldziej, Jaroslaw Pillardy, Cezary Czaplewski, Adam Liwo, Daniel R. Ripoll
Publikováno v:
Frontiers in bioscience : a journal and virtual library. 9
The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the development of a suitable empirical all-atom potential energy function and a global optimization
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc79d52d8493701b0e59f6bf43a75406
https://pubmed.ncbi.nlm.nih.gov/15353359
https://pubmed.ncbi.nlm.nih.gov/15353359
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