1997
DOI: 10.1002/(sici)1096-987x(199705)18:7<874::aid-jcc2>3.0.co;2-o
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A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization

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Cited by 191 publications
(313 citation statements)
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“…By reducing the number of degrees of freedom, coarse-grained models of proteins can drastically reduce the intrinsic cost of simulating a time step, as well as increasing the duration of each step. The strategy has been pursued for many different problems over the years from protein folding to aggregation to conformational change (8,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Although coarse-grained models fail to capture atomistic detail and may have limited biochemical accuracy, recent work may permit the use of simplified ensembles in accelerating atomistic sampling (28,29).…”
mentioning
confidence: 99%
“…By reducing the number of degrees of freedom, coarse-grained models of proteins can drastically reduce the intrinsic cost of simulating a time step, as well as increasing the duration of each step. The strategy has been pursued for many different problems over the years from protein folding to aggregation to conformational change (8,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Although coarse-grained models fail to capture atomistic detail and may have limited biochemical accuracy, recent work may permit the use of simplified ensembles in accelerating atomistic sampling (28,29).…”
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confidence: 99%
“…The UNRES model of polypeptide chains and the associated energy function are described in our earlier papers (11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29), and only a brief summary is presented here. The polypeptide chain is represented as a sequence of ␣-carbon atoms (C ␣ ) linked by virtual bonds of length 3.8 Å corresponding to trans peptide groups.…”
Section: Methodsmentioning
confidence: 99%
“…14). The parameters of U SCSC , U b , and U rot were derived (14,15) from the distribution and correlation functions calculated from the PDB (38), whereas those of U corr (i) , Ϫi ϭ 3,4,5,6, U tor , U tord , and U pp were calculated by fitting the corresponding analytical expression to the restricted free energy surfaces of model all-atom systems calculated by using high-level quantum-mechanical ab initio methods (25,26). Use of protein-structural data is not, however, necessary to derive the parameters of U SCSC , U b , and U rot , and was motivated only by lack of sufficient resources; these terms are currently being reparameterized based on the results of our simulation studies of the potentials of mean force of models of SC in water (39,40) and quantum-mechanical calculations of the energy surfaces of terminally blocked amino acid residues (25), respectively.…”
Section: Methodsmentioning
confidence: 99%
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“…In protein folding studies, knowledge-based potentials derived from a statistical analysis of known protein structures (Ueda et al, 1978;Maiorov & Crippen, 1992;Kolinski & Skolnick, 1994;Sippl, 1995; Mimy & Domany, 1996;Miyazawa & Jernigan, 1996;Liwo et al, 1997;Park et al, 1997) are frequently used in simplified models of proteins. The quality of such potentials is often assessed by socalled Z-scores, which test how well the potentials differentiate the native fold of a protein from an ensemble of misfolded structures.…”
Section: Abstract: Knowledge-based Potentials; Protein Folding; Z-scoresmentioning
confidence: 99%