Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., Bourne, P.: The protein data bank. Nucleic Acids Research 28 (2000) 235--42 Home/Search Document Not in Database Summary Related Articles Check |
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EIMaR: A Protein Docking System using Flexibility.. - Zöllner, Neumann.. (2002) (Correct)
....or proteins. Docking Algorithms try to answer the question if and how two proteins interact with each other. For two given proteins the problem is known as 1:1 protein docking . For database searches, where an appropriate docking partner is searched in a potentially large database like the PDB [3] this is the 1 :N protein docking . For database searches it is not always neccessary to retrieve the complete result set. Depending on the application the goal can be Find any one Protein that docks, false negatives allowed or Find at least all Proteins that dock, false positives allowed ....
H. M. Bermann, J. Westbrook, E Zukang, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindylalov, and R E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000.
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....in the initial studies [11] of matching between the protein sites and sites on the canonic B form DNA. We developed model of the DNA deformation that reproduces the conformation of the experimental structure. The most common deformations in the structures from the Protein Data Bank (PDB) [7] bring bases in the base pairs out of the canonic plane. Example is a propeller twist where two flat bases rotate opposite each other (see Figure 3.1) Each base is connected to the backbone by the bond between N1 and C1 atoms. The bond between N1 and C1 is denoted with an arrow on Figures ....
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Wessig, 74 I.N. Shidyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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....joining two amino acids when synthesizing a protein. The functional properties of proteins depend upon their three dimensional structures. Understanding and predicting these structures has proven quite daunting, despite the fact that the structure of thousands of proteins have been determined [11]. Unlike the structure of other biological macromolecules (e.g. DNA) proteins have complex, irregular structures. Our focus in the this section is on globular proteins, which exhibit a speci c native state. The sequence of residues in a protein is called its primary structure. A variety of ....
H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28:235242, 2000. The PDB is at http://www.rcsb.org/pdb/.
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....city measures. The CC value is de ned in the interval [ 1 : 1] the extreme value 1 represents poor prediction accuracy (random) and 1 represents a good prediction accuracy (perfect) 4. 1 Sequence Data The protein sequences used for the training set were taken from the Protein Data Bank (PDB) [10], release 82. This data set, containing 5762 proteins, was further reduced to ensure that all the sequences were not homologous, i.e. entries were excluded if they were too similar. The reduction was performed by the RedHom program [11] resulting in a nal training set containing 650 sequences ....
Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I.N., and Bourne, P.: The Protein Data Bank. Nucleic Acids Research, Vol. 28, No. 1. (2000) 235-242
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....RPI Exploratory Seed Grant, NSF CAREER Award IIS 0092978, and NSF Next Generation Software Program grant EIA 0103708. Instead of simulation studies, an alternative approach is to employ learning from examples using a database of known protein structures. For example, the Protein Data Bank (PDB) [2] records the 3D coordinates of the atoms of thousands of protein structures. Most of these proteins cluster into around 700 fold families based on their similarities. It is conjectured that there will be on the order of 1000 fold families for the natural proteins [8] The PDB thus offers a new ....
H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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....and are important for oxygen storage and transport. Third, we used 6 sequences of the protein cytochrome C. These proteins are involved in electron transport and are also quite well conserved. All the protein sequences were collected from the wellknown public accessible Protein Data Bank (PDB) [1]. The PDB entries for each of the sequences are shown in the appendix. B. Experimental Setup and Data Sampling We used the following parameters in the MSA EA: population size = 150 mutation probability = 0.7 crossover probability = 0.8 Further, we set the termination criteria of the ....
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, Vol. 28, No. 1, pp. 235{ 242, 2000.
Multimeme Algorithms for the Structure Prediction and.. - Krasnogor, Smith (2002) (1 citation) (Correct)
.... Protein Structure Comparison The MMA used for the alignment of contact maps is fully described in [2] We tested the behavior of both a GA ( that follows as close as possible the implementation described in [13] and our MMA in a set of 18 pairs of proteins downloaded from the protein data bank[1]. The total number of tness evaluations allocated to the algorithms was 5 10 6 . The upper bound found by the linear programming approach of Lancia et.al was also computed. We will present results showing that out of 18 protein pairs the GA outperformed the MMA in just one case. The MMA ....
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissing, I.N. Shindyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000.
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....diagonal. A 0 1 contact map can also be represented as an undirected graph. In this graph, each residue is a node and there exists an edge between nodes i and j if these residues are in contact (i.e. if S i;j = 1) Figure 2 The proteins used in this paper are taken from the Protein Data Bank [1], and the labels we use are the labels provided by the PDB. helices and sheets are elements of a protein s secondary structure. See [2] for a description of protein secondary structure. Figure 1: A 0 1 contact map comparing protein 1C7W with itself. shows the native structures of two ....
....crossover probabilities were not optimized for the Multimeme code but as mentioned before, taken from the GA setting. The innovation rate for the Multimeme algorithm was 1.0 and 0. 15 (see below) We performed two experiments on a set of 18 pairs of protein structures from the Protein Data Bank [1]. For these 18 pairs we had the upper bound values ob 1avy 1bct 19 22 25 1b6w 1bw5 23 23 24 1bct 1bw5 20 17 20 1bct 1f22 20 18 22 1bct 1ilp 18 18 23 1c7v 1c7w 62 62 62 1c9o 1kdf 29 29 40 1df5 1f22 21 22 27 1hlh 1hrf 19 21 24 1hlh 1nmf 22 22 27 1kst 2new 20 22 26 1nmf 2new 23 23 27 ....
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissing, I.N. Shindyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000.
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne. The Protein Data Bank. Nucleic Acids Research 28:235--242, 2000.
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Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shindyalov, I., Bourne, P.: The protein data bank. Nucleic Acids Research 28 (2000) 235--42
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H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, (28):235--242, 2000.
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H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, (28):235--242, 2000.
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. The Protein Data Bank. Nucleic Acids Research, 28 (2000) 235-242. - http://www.rcsb.org/pdb/index.html
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov and P.E. Bourne, The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242, 2000
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. The Protein Data Bank. Nucleic Acids Research, 28:235-242 (2000)
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissing, I.N. Shindyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-- 242, 2000.
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H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, (28):235--242, 2000.
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne. The Protein Data Bank. Nucleic Acids Research, 28:235{ 242, 2000.
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H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The protein data bank. Nucleic Acids Research, 28:235--242, 2000.
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H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne, The Protein Data Bank, Nucleic Acids Research, 28 pp. 235-242, 2000.
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