메뉴 건너뛰기




Volumn 30, Issue 6, 2012, Pages 773-783

HELANAL-Plus: A web server for analysis of helix geometry in protein structures

Author keywords

A helix; Geometry of the helix; Helix axis; JmolApplet; UP DOWN ring conformation of Proline

Indexed keywords

MEMBRANE PROTEIN; PROLINE; SERINE; THREONINE;

EID: 84871241613     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.689705     Document Type: Article
Times cited : (58)

References (37)
  • 2
    • 0022583145 scopus 로고
    • A simple way to calculate the axis of an α-helix
    • Åqvist, J. (1986). A simple way to calculate the axis of an α-helix. Computers & Chemistry, 10, 97-99.
    • (1986) Computers & Chemistry , vol.10 , pp. 97-99
    • Åqvist, J.1
  • 3
    • 0033747337 scopus 로고    scopus 로고
    • Serine and threonine residues bend alphahelices in the chi(1) = g(-) conformation
    • Ballesteros, J.A., Deupi, X., Olivella, M., Haaksma, E.E., & Pardo, L. (2000). Serine and threonine residues bend alphahelices in the chi(1) = g(-) conformation. Biophysal Journal, 79, 2754-2760.
    • (2000) Biophysal Journal , vol.79 , pp. 2754-2760
    • Ballesteros, J.A.1    Deupi, X.2    Olivella, M.3    Haaksma, E.E.4    Pardo, L.5
  • 7
    • 0021062575 scopus 로고
    • Solvent-induced distortions and the curvature of alpha-helices
    • Blundell, T., Barlow, D., Borkakoti, N., & Thornton, J. (1983). Solvent-induced distortions and the curvature of alpha-helices. Nature, 306, 281-283.
    • (1983) Nature , vol.306 , pp. 281-283
    • Blundell, T.1    Barlow, D.2    Borkakoti, N.3    Thornton, J.4
  • 8
    • 0033977581 scopus 로고    scopus 로고
    • The astral compendium for protein structure and sequence analysis
    • Brenner, S.E., Koehl, P., & Levitt, M. (2000). The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Research, 28, 254-256.
    • (2000) Nucleic Acids Research , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3
  • 9
    • 0022732199 scopus 로고
    • Peptidebond distortions and the curvature of alpha-helices
    • Chakrabarti, P., Bernard, M., & Rees, D.C. (1986). Peptidebond distortions and the curvature of alpha-helices. Biopolymers, 25, 1087-1093.
    • (1986) Biopolymers , vol.25 , pp. 1087-1093
    • Chakrabarti, P.1    Bernard, M.2    Rees, D.C.3
  • 10
    • 0032509022 scopus 로고    scopus 로고
    • C-H.O Hydrogen bond involving proline residues in alpha-helices
    • Chakrabarti, P., & Chakrabarti, S. (1998). C-H.O hydrogen bond involving proline residues in alpha-helices. Journal of Molecular Biology, 284, 867-873.
    • (1998) Journal of Molecular Biology , vol.284 , pp. 867-873
    • Chakrabarti, P.1    Chakrabarti, S.2
  • 11
    • 0034994293 scopus 로고    scopus 로고
    • The interrelationships of side-chain and main-chain conformations in proteins
    • Chakrabarti, P., & Pal, D. (2001). The interrelationships of side-chain and main-chain conformations in proteins. Progress in Biophysics and Molecular Biology, 76, 1-102.
    • (2001) Progress in Biophysics and Molecular Biology , vol.76 , pp. 1-102
    • Chakrabarti, P.1    Pal, D.2
  • 13
    • 0030239753 scopus 로고    scopus 로고
    • Algorithms for finding the axis of a helix: Fast rotational and parametric least-squares methods
    • Christopher, J.A., Swanson, R., & Baldwin, T.O. (1996). Algorithms for finding the axis of a helix: Fast rotational and parametric least-squares methods. Computers & Chemistry, 20, 339-345.
    • (1996) Computers & Chemistry , vol.20 , pp. 339-345
    • Christopher, J.A.1    Swanson, R.2    Baldwin, T.O.3
  • 16
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman, D., & Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 17
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 18
    • 0024921948 scopus 로고
    • Defining the axis of a helix
    • Kahn, P.C. (1989). Defining the axis of a helix. Computers & Chemistry, 13, 185-189.
    • (1989) Computers & Chemistry , vol.13 , pp. 185-189
    • Kahn, P.C.1
  • 19
    • 0001266102 scopus 로고
    • A three-dimensional model of the myoglobin molecule obtained by x-ray analysis
    • Kendrew, J.C., Bodo, G., Dintzis, H.M., Parrish, R.G., Wyckoff, H., & Phillips, D.C. (1958). A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature, 181, 662-666.
    • (1958) Nature , vol.181 , pp. 662-666
    • Kendrew, J.C.1    Bodo, G.2    Dintzis, H.M.3    Parrish, R.G.4    Wyckoff, H.5    Phillips, D.C.6
  • 21
    • 0029738679 scopus 로고    scopus 로고
    • Structural and sequence characteristics of long alpha helices in globular proteins
    • Kumar, S., & Bansal, M. (1996). Structural and sequence characteristics of long alpha helices in globular proteins. Biophysical Journal, 71, 1574-1586.
    • (1996) Biophysical Journal , vol.71 , pp. 1574-1586
    • Kumar, S.1    Bansal, M.2
  • 22
    • 0031660702 scopus 로고    scopus 로고
    • Geometrical and sequence characteristics of alpha-helices in globular proteins
    • Kumar, S., & Bansal, M. (1998). Geometrical and sequence characteristics of alpha-helices in globular proteins. Biophysical Journal, 75, 1935-1944.
    • (1998) Biophysical Journal , vol.75 , pp. 1935-1944
    • Kumar, S.1    Bansal, M.2
  • 23
    • 78650702465 scopus 로고    scopus 로고
    • Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors
    • Langelaan, D.N., Wieczorek, M., Blouin, C., & Rainey, J.K. (2010). Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. Journal of Chemical Information and Modeling, 50, 2213-2220.
    • (2010) Journal of Chemical Information and Modeling , vol.50 , pp. 2213-2220
    • Langelaan, D.N.1    Wieczorek, M.2    Blouin, C.3    Rainey, J.K.4
  • 25
    • 0030596007 scopus 로고    scopus 로고
    • Deviations from planarity of the peptide bond in peptides and proteins
    • MacArthur, M.W., & Thornton, J.M. (1996). Deviations from planarity of the peptide bond in peptides and proteins. Journal of Molecular Biology, 264, 1180-1195.
    • (1996) Journal of Molecular Biology , vol.264 , pp. 1180-1195
    • MacArthur, M.W.1    Thornton, J.M.2
  • 26
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald, I.K., & Thornton, J.M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology, 238, 777-793.
    • (1994) Journal of Molecular Biology , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 27
    • 33745167012 scopus 로고    scopus 로고
    • Trajelix: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations
    • Mezei, M., & Filizola, M. (2006). TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations. Journal of Computer-Aided Molecular Design, 20, 97-107.
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , pp. 97-107
    • Mezei, M.1    Filizola, M.2
  • 28
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. Vii. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
    • Momany, F.A., McGuire, R.F., Burgess, A.W., & Scheraga, H. A. (1975). Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. Journal of Physical Chemistry, 79, 2361-2381.
    • (1975) Journal of Physical Chemistry , vol.79 , pp. 2361-2381
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 30
    • 0025059332 scopus 로고
    • Conformational studies on peptides with proline in the right-handed alpha-helical region
    • Sankararamakrishnan, R., & Vishveshwara, S. (1990). Conformational studies on peptides with proline in the right-handed alpha-helical region. Biopolymers, 30, 287-298.
    • (1990) Biopolymers , vol.30 , pp. 287-298
    • Sankararamakrishnan, R.1    Vishveshwara, S.2
  • 33
    • 84984088684 scopus 로고
    • General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal rotation angles
    • Sugeta, H., & Miyazawa, T. (1967). General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal rotation angles. Biopolymers, 5, 673-679.
    • (1967) Biopolymers , vol.5 , pp. 673-679
    • Sugeta, H.1    Miyazawa, T.2
  • 34
    • 13444280419 scopus 로고    scopus 로고
    • Pdb-Tm: Selection and membrane localization of transmembrane proteins in the protein data bank
    • Tusnady, G.E., Dosztanyi, Z., & Simon, I. (2005a). PDB-TM: Selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Research, 33, D275-278.
    • (2005) Nucleic Acids Research , vol.33
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 35
    • 16344362822 scopus 로고    scopus 로고
    • Tmdet: Web server for detecting transmembrane regions of proteins by using their 3d coordinates
    • Tusnady, G.E., Dosztanyi, Z., & Simon, I. (2005b). TMDET: Web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics, 21, 1276-1277.
    • (2005) Bioinformatics , vol.21 , pp. 1276-1277
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 36
    • 0033768889 scopus 로고    scopus 로고
    • Prokink: A protocol for numerical evaluation of helix distortions by proline
    • Visiers, I., Braunheim, B.B., & Weinstein, H. (2000). Prokink: A protocol for numerical evaluation of helix distortions by proline. Protein Engineering, 13, 603-606.
    • (2000) Protein Engineering , vol.13 , pp. 603-606
    • Visiers, I.1    Braunheim, B.B.2    Weinstein, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.