Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI and Dill KA (1995) A test of lattice protein folding algorithms. Proc Natl Acad Sci 92:325-329.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....Molecular conformation of L chicoric acid produced by the program under the Dreiding atomic force field [13] with implicit solvent [12] 3. 2 Comparative Performance Table 1 shows the algorithm working under the HP cubic lattice model compared to previously published HP cubic lattice methods [1, 5, 15, 16] on 10 previously published HP sequences [16] The sequences are all 48 HP residues long, resulting in a search space size of 5 46 32 . The sequences, as well as the scores shown for Native, PNS, and HZ, are taken from reference [16] The score for CGA is taken from the first conformation ....

....by the program under the Dreiding atomic force field [13] with implicit solvent [12] 3. 2 Comparative Performance Table 1 shows the algorithm working under the HP cubic lattice model compared to previously published HP cubic lattice methods [1, 5, 15, 16] on 10 previously published HP sequences [16]. The sequences are all 48 HP residues long, resulting in a search space size of 5 46 32 . The sequences, as well as the scores shown for Native, PNS, and HZ, are taken from reference [16] The score for CGA is taken from the first conformation produced by the multi queue algorithm; it uses ....

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Yue, K., Fiebig, K.M., Thomas, P.D., Chan, H.S., Shakhnovich, E.I., and Dill, K.A., A test of lattice protein folding algorithms, Proc. Natl. Acad. Sci. USA, 92:325--329, 1995.

....average contact energy between any two amino acids must be attractive; only then one gets proteins whose native structure is on the 3 3 3 cube with high probability (see [21] 2. even then, it is not guaranteed that the minimal conformation is on this cube (for examples in the HP model see [24]) 3. the length of the proteins cannot be arbitrarily chosen. 1.1 Previous Work In the literature, several algorithms were proposed for the HP model, and we will discuss some of them. One class of algorithm consists of heuristic methods. There are heuristic approaches such as the hydrophobic ....

Kaizhi Yue, M. Fiebig, Poaul D. Thomas, Hue Sun Chan, Eugene I. Shakhnovich, and Ken A. Dill. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA, 92:325 - 329, 1995. 34

....1. The energy function had to be biased to a mean hydrophobicity in order to get proteins whose native structure is on the 3 Theta 3 Theta 3 cube with high probability (see [19] 2. even then, it is not guaranteed that the minimal conformation is on this cube (for examples in the HP model see [22]) 3. the length of the proteins cannot be arbitrarily chosen. 1.1 Previous Work In the literature, several algorithms were proposed for the HP model, and we will discuss some of them. One class of algorithm consists of heuristic methods. monte carlo, hydrophobic zipper, chain growth there are ....

Kaizhi Yue, M. Fiebig, Poaul D. Thomas, Hue Sun Chan, Eugene I. Shakhnovich, and Ken A. Dill. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA, 92:325 -- 329, 1995. 34

....of the energy function is a species dependent term that favors the formation of a hydrophobic core. However, as will be demonstrated below, this term alone is not sufficient in order to have thermodynamically dominant native states. This observation is reminiscent of existing lattice model results [5, 6], and could be taken as an indication that it is essential to have more than two different types of amino acids. In this paper we explore another possibility; do the folding properties depend on species independent local interactions sticking to two amino acid types only It should be noted that ....

....high folding temperature is accompanied by a relatively low temperature for the peak of the specific heat. This is in contrast to what has been previously reported. 8] Finally, we stress the fact that we have studied sequences with only two types of residues. In the work by Shakhnovich et al. [5, 6] a number of binary (two letter code) sequences were studied in a 3D lattice model. The two letter code was found to be insufficient in the sense that these sequences did not have unique native structures. In our model, many binary sequences do have unique native structures. Our ability to map out ....

K. Yue, K.M. Fiebig, P.D. Thomas, H.S. Chan, E.I. Shakhnovich and K.A. Dill, "A Test of Lattice Protein Folding Algorithms", Proc. Natl. Acad. Sci. USA 92, 325 (1995).

....and it has been found that the degree of heterogeneity plays an important role. For example, for the cubic lattice, it has been shown that it is possible to design twenty letter sequences that have unique native structures, whereas two letter sequences with this property seem to be rare [4, 5]. However, a limitation of these models is that local interactions are neglected, and such interactions might be important not only for the local structure of the chains, as illustrated by a recent study of a simple three dimensional off lattice model [6] This model, with a simple two letter ....

K. Yue, K.M. Fiebig, P.D. Thomas, H.S. Chan, E.I. Shakhnovich and K.A. Dill, "A Test of Lattice Protein Folding Algorithms", Proc. Natl. Acad. Sci. USA 92, 325 (1995).

....that is shifted through the sequence and recursively counts up low energy states. Further algorithms are the hydrophobic zipper model, proposed by Fiebig et al. which starts with a random HH contact and zips up the rest [15, 14] Another, branch and bound like algorithm designed by Yue et al. [45] constructs an ensemble of cores that fits within some, theoretically approximated, bounds and follows some constraints. It is extremely successful but computationally demanding [45] None of these algorithms seem to be fast enough for statistical investigations of large ensembles of random ....

....random HH contact and zips up the rest [15, 14] Another, branch and bound like algorithm designed by Yue et al. 45] constructs an ensemble of cores that fits within some, theoretically approximated, bounds and follows some constraints. It is extremely successful but computationally demanding [45]. None of these algorithms seem to be fast enough for statistical investigations of large ensembles of random structures. Hart and Istrail [19] recently presented an algorithm for the HP model that guarantees structures with energy better than 3=8 of optimum. Accuracy depends strongly on the ....

[Article contains additional citation context not shown here]

K. Yue, M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci., USA, 92:325 -- 329, 1995.

....sequences studied. This observatoin is Figure 8: The distribution P (ffi 2 ) for one sequence with different types of local interaction: 1 ; 2) 0; 0) dots) 1,0) dashes) and ( 1,0.5) solid) T = 0:15. The low peak for ( 1,0.5) extends to 37. reminiscent of existing lattice model studies [13, 16] and could be taken as an indication that it is necessary to have more than two types of amino acids. Here we have explored another possibility, good folding sequences can be obtained by including local interactions. Several other settings of ( 1 ; 2 ) have been tested, all giving rise to higher ....

Yue, Kaizhi, Klaus M. Fiebig, Paul D. Thomas, Hue Sun Chan, Eugene I. Shakhnovich, and Ken A. Dill "A test of lattice protein folding algorithms", Proc. Natl. Acad. Sci. USA 92 (1995), 325--329.

.... to a native state, chains have much conformational freedom and the self avoiding walk constraint accounts for steric restrictions (excluded volume effect) HP sequences in general show a large structural degeneracy i.e. the number of configurations that correspond to one lowest energy state [9, 35]. For n = 18 on a square lattice only ca. 2.4 of all chains fall into a unique ground state. This is remarkable since real proteins, synthesized from binary patterns, also frequently appear with little structural specifity [7] A detail study on the influence for 2 letter alphabets was recently ....

....and zips up nearby contacts. It was claimed to yield molten globe like structures [10, 9] A branch and bound algorithm designed by Yue et al. finds the ground state by constructing ensembles of cores that fit within some, theoretically approximated bounds and follows several constraints [35]. None of these algorithms seem to be fast enough for statistical investigations of large ensembles. Hart and Istrail recently presented a fast algorithm with performance guarantee that yields not very compact chains. It is deterministic, works in O(n) but neglects different potentials and cross ....

K. Yue, M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill. A test of lattice protein folding algorithms. Proc.Natl.Acad.Sci.USA, 92:325 -- 329,

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Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI and Dill KA (1995) A test of lattice protein folding algorithms. Proc Natl Acad Sci 92:325-329.

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Yue, K., Fiebig, K.M., Thomas, P.D., Sun, C.H., Shakhnovich, E.I., Dill, K.A.: A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA 92 (1995) 325--329

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Yue, K., Fiebig, K.M., Thomas, P.D., Sun, C.H., Shakhnovich, E.I., Dill, K.A.: A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. USA 92 (1995) 325--329

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Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. 1995;92:325--329. A Simplified Model for Protein Folding 12

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Yue, K., Fiebig, K., Thomas, P., Chan, H., Shakhnovich, E., & Dill, K. (1995). A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. 92, 325--329.

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Yue, K., et al. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci. U.S.A. 92:325, 1995.

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K. Yue, K.M. Fiebig, P.D. Thomas, H.S. Chan, E.I. Shakhnovich and K.A. Dill, "A Test of Lattice Protein Folding Algorithms", Proc. Natl. Acad. Sci. USA 92, 325--329 (1995).

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Biol. 241:557 -- 573. Yue, K., M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich and K. A. Dill, 1995. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci., USA 92:325 -- 329.

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