Bernstein, F. C.; Koetzle, T. F.; Williams, J. B.; Meyer Jr., E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; and Tasumi, M. 1977. The Protein Data Bank: A computer-- based archival file for macromolecular structures. Journal of Molecular Biology 112:535--542. Home/Search Document Not in Database Summary Related Articles Check |
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Protein Sidechain Conformer Prediction: A Test of the.. - Petrella, Lazaridis.. (1998) (1 citation) (Correct)
....function explored in this study could be applied usefully to many sidechain prediction methods to establish upper limits of accuracy. Materials and methods Selection and preparation of protein structures Ten protein crystal structures (Table 11) were chosen from the Brookhaven Protein Data Bank [58]. They were selected because they have all been used in sidechain prediction studies, with the exception of the HIV 1 protease. All are at a resolution of 2 or better with the exception of the Cro repressor structure, and all were refined with stereochemically restrained refinement techniques such ....
Bernstein, F.C., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
Finding Patterns in Three Dimensional Graphs.. - Wang, Wang.. (2002) (6 citations) (Correct)
....if we consider a protein as a 3D graph, each node of the graph is an atom. Each node has a label, which is the name of the atom and is not unique in the protein. We assign a unique number to identify a node in the protein, where the order of numbering is obtained from the Protein Data Bank (PDB) [1, 2], accessible at http: www.rcsb.org. In the experiments, we examined two families of proteins chosen from PDB pertaining to RNA directed DNA Polymerase and Thymidylate Synthase. Each family contains proteins having the same functionality in various organisms. We decompose each protein into ....
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, "The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures," J. Molecular Biology, Vol. 112, 1977, pp. 535--542.
Expert Antibody Side Chain Placement - Ritchie (Correct)
....be correct) 2.4.4 Dead end Elimination One of the more mathematical techniques is the Dead End Elimination (DEE) algorithm of Desmet et al. 10] This also makes use of a rotamer library but in a somewhat novel way. The basic principle is to eliminate candidate rotamers The Protein Data Bank [2] at Brookhaven is one of the main protein structure libraries. CHARMM [4] is the molecular dynamics module of the QUANTA package. 18 on energetic considerations. All energy based approaches attempt to solve for the minimum energy conformation of the system. In terms of rotamer search, Desmet ....
....was given as a table of torsion angles. In his 1991 MSc. project, Georgios Lappas [18] converted the library into a list of explicit atom coordinates, formatted as a P FDM load file. He produced these coordinates by backcalculating from the Desmet angles and some bond lengths taken from the PDB [2], although the precise details were not given. z y x C a N Rotamer C C a N ResidueA ResidueB (c) Figure 3.4: The C ff C N coordinate system. a) b) and (c) represent useful transformations. This P FDM load file is also used in the current project. However, each rotamer was ....
Bernstein F.C., Koetzle T.F., Williams G.J.B., Mayer E.F. Jr, Bryce M.D., Rodgers J.R., Kennard O., Shimanouchi T., Tasumi M. (1977), The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, J. Mol. Biol. 112 535--542.
HAKKE: A Multi-Strategy Prediction System for Sequences - Furukawa, Matsumoto.. (Correct)
....higher than that without using abstention. Table 1: Results on transmembrane domain sequences generated predictor (with abstention) 91.6 54.6 94.6 45.6 96.2 0.207 generated predictor (without abstention) 87.9 65.5 89.8 34.6 96.9 0.173 5.2. 2 ff helices We used the PDB database [8] that contains the amino acid sequences associated with their three dimensional coordinates. By using the DSSP program [9] which translates three dimensional coordinates into the secondary structures, we marked the positions of ff helices in the amino acid sequences. We regarded the ff helices as ....
F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. E. Meyer Jr, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi, "The Protein Data Bank: a Computer-Based Archival File for Macromolecular Structures," J. Mol. Biol.,Vol. 112, pp. 535--542, 1977.
Searches for Topologically and Three Dimensionally.. - Satou, Furuichi.. (Correct)
.... ) 108 El5 ET9A6hGr6bBf 4 6 1 1 Introduction To clarify relationships between structure and function of protein, crystallographic determined conformations of protein have to be analyzed. The main source of these data is Brookhaven s Protein Data Bank(PDB)[1]. To properly handle PDB data, several prototype databases were developed[3, 6, 7, 2] To deal with coordinates of protein, a proper representation of the structure of protein is important. We developed a deductive database system PACADE (Protein Coordinate Analyzer with Deductive Engine) for ....
Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M.: The Protein Data Bank: A Computerbased Archival File for Macromolecular Structures, Journal of Molecular Biology, 112, pp.535-542 (1977).
New Hashing Techniques for Three-Dimensional Protein.. - Akutsu, Onizuka, Ishikawa (1994) (Correct)
....is small. Thus, we have developed new hashing methods, in which the above property is theoretically proved. As far as we know, the proposed hash vectors are the first ones for which the above property is theoretically proved. Moreover, experimental results using PDB (Protein Data Bank) data [3] show that the new methods are much faster than the naive method and the least squares hashing method. 2 Preliminaries In this paper, protein structures are treated as follows. As we are only interested in representing an outline of 3D structure, we follow the common procedure of ignoring side ....
....that it does not fail to find similar fragments even if a much smaller value is used. It is obvious that the search time is reduced if a smaller fl is used. Thus, the value for fl should be determined based on experimental results. 4 Experimental Results Experiments have been done using PDB data [3]. Although PDB data contain various kinds of information, only positions of Cff atoms are used. All algorithms are implemented in the C language on a SUN SPARC STATION 10 (a UNIX workstation) New hashing methods are compared with the previous and the naive ones in Table 1. NV denotes the naive ....
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi, "The Protein Data Bank: A computer-based archival file for macromolecular structures," J. Molecular Biology, Vol. 112, pp. 535-542, 1976.
Similar Structure Search in a Deductive Database - Kenji Satou Emiko (1993) (Correct)
....root mean square distance. The outline of the function and some results of searches for super secondary structure, using the function are given herein, in detail. 1 Introduction Crystallographically determined atomic coordinates of protein are preserved in Brookhaven s Protein Data Bank (PDB) [2]. In proportion to the size of PDB, a database system plays an important role in searches for large amounts of data on these three dimensional structures. With growth in these numbers, research on relationships between structure and function of protein has also greatly advanced. If the same ....
Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M.: The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, Journal of Molecular Biology, 112, pp.535-542 (1977).
Stochastic Conformational Roadmaps for Computing.. - Apaydin, Brutlag, .. (2004) (1 citation) (Correct)
....on all 10,000 conformations, we can easily infer that that the running time would be around 800,000 seconds. 1ROP and 1HDD We also tested SRS on two real proteins (Fig. 4) repressor of primer and engrailed homeodomain, which are identified as 1ROP and 1HDD, respectively, in the Protein Data Bank [7]. 1ROP is a dimer that consists of two identical parts called monomers. As in [30] we study one monomer in isolation. The monomer contains 56 residues forming two helices connected by a loop. 1HDD contains 57 residues forming three helices packed against each other. Our implementation represents ....
F.C. Bernstein et al. The protein data bank: A computer-based archival file for macromolecular structure. J. Mol. Biol., 112(3):535--542, 1977.
Stochastic Roadmap Simulation: An Efficient.. - Apaydin, Brutlag, .. (2002) (5 citations) (Correct)
....than that of computing any reasonable energy function for a real protein. 5.2. 2 1ROP and 1HDD More interestingly, we also tested SRS on two real proteins (Figure 7) repressor of primer and engrailed homeo domain, which are identified as 1ROP and 1HDD, respectively, in the Protein Data Bank [B 77] 1ROP is a dimer made of two identical monomers, each containing 56 residues forming two helices connected by a loop. As in [STD95] we study a single monomer in isolation. Protein 1HDD contains 57 residues forming three helices packed against each other. Our implementation encodes the ....
F.C. Bernstein et al. The protein data bank: A computer-based archival file for macromolecular structure. J. Mol. Biol., 112(3):535--542, 1977.
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Bernstein, F. C.; Koetzle, T. F.; Williams, J. B.; Meyer Jr., E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; and Tasumi, M. 1977. The Protein Data Bank: A computer-- based archival file for macromolecular structures. Journal of Molecular Biology 112:535--542.
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Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, Jr., E.E., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M., The protein data bank: A computer-based archival file for macromolecular structures, J. Mol. Biol., 112:535--542, 1977.
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Bernstein, F.C., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
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F.C. Bernstein, T.F. Koetzle, G.J. Williams, E.E.J. Meyer, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tsumi. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535--542, 1977.
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Bernstein, F., Koetzle, T., Williams, G., Meyer, E., Brice, M., Rodgers, J. et al. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535 -- 542.
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Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanovichi T., Tasumi M.: `The Protein Data Bank: a Computer-based Archival File for Macromolecular Structures', Journal of Molecular Biology, Vol. 112, 1977, pp. 535-542.
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Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M., The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., Vol. 112 (1977) 535-542
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Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M.: The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., Vol. 112 (1977) 535-542
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Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanovichi T., Tasumi M.: `The Protein Data Bank: a Computer-based Archival File for Macromolecular Structures', Journal of Molecular Biology, Vol. 112, 1977, pp. 535-542.
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Bernstein, F.C., T.F. Koetzle, G.J. Williams, E.E. Meyer, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi (1977): The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures. J. Mol. Biol., 112, 535-542.
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Bernstein F, Koetzle T, Williams G, Meyer EJ, Brice M, Rodgers J, Kennard O, Shimanouchi T, and Tasumi M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 1977; 112:535--542.
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F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, J. E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol., 112:535--542, 1977.
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Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Brice M. D., Rodgers J. R., Kennard O., Shimanovichi T., Tasumi M.: `The Protein Data Bank: a Computer-based Archival File for Macromolecular Structures', Journal of Molecular Biology, Vol. 112, 1977, 535-542.
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Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., Jr., Brice M.D., Rodgers J.R., Kennard O., Shimanouchi T., and Tasumi M., The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, J.Mol.Biol., 112, 535-542 (1977).
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Bernstein,F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) The protein data bank: a computer-based archival file for macro-molecular structure. J. Mol. Biol., 112, 535--542.
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Bernstein,F.C., Koetzle,T.F., Williams,G.J., Meyer,E.E., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535--542.
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