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

References

• Andreeva , A. , Howorth , D. , Chandonia , J.M. , Brenner , S.E. , Hubbard , T.J. , Chothia , C. and Murzin , A.G. 2008 . Data growth and its impact on the SCOP database: New developments . Nucleic Acids Research , 36 : D419 – 425 .
   PubMed Web of Science ®Google Scholar
• Åqvist , J. 1986 . A simple way to calculate the axis of an α-helix . Computers & Chemistry , 10 : 97 – 99 .
   Google Scholar
• Ballesteros , J.A. , Deupi , X. , Olivella , M. , Haaksma , E.E. and Pardo , L. 2000 . Serine and threonine residues bend alpha-helices in the chi(1) = g(−) conformation . Biophysal Journal , 79 : 2754 – 2760 .
   PubMed Web of Science ®Google Scholar
• Bansal , M. , Kumar , S. and Velavan , R. 2000 . HELANAL: A program to characterize helix geometry in proteins . Journal of Biomolecular Structure & Dynamics , 17 : 811 – 819 .
   PubMed Web of Science ®Google Scholar
• Barlow , D.J. and Thornton , J.M. 1988 . Helix geometry in proteins . Journal of Molecular Biology , 201 : 601 – 619 .
   PubMed Web of Science ®Google Scholar
• Berman , H.M. , Westbrook , J. , Feng , Z. , Gilliland , G. , Bhat , T.N. , Weissig , H. , … and Bourne , P.E. 2000 . The protein data bank . Nucleic Acids Research , 28 : 235 – 242 .
   PubMed Web of Science ®Google Scholar
• Blundell , T. , Barlow , D. , Borkakoti , N. and Thornton , J. 1983 . Solvent-induced distortions and the curvature of alpha-helices . Nature , 306 : 281 – 283 .
   PubMed Web of Science ®Google Scholar
• Brenner , S.E. , Koehl , P. and Levitt , M. 2000 . The ASTRAL compendium for protein structure and sequence analysis . Nucleic Acids Research , 28 : 254 – 256 .
   PubMed Web of Science ®Google Scholar
• Chakrabarti , P. , Bernard , M. and Rees , D.C. 1986 . Peptide-bond distortions and the curvature of alpha-helices . Biopolymers , 25 : 1087 – 1093 .
   PubMed Web of Science ®Google Scholar
• Chakrabarti , P. and Chakrabarti , S. 1998 . C–H...O hydrogen bond involving proline residues in alpha-helices . Journal of Molecular Biology , 284 : 867 – 873 .
   PubMed Web of Science ®Google Scholar
• Chakrabarti , P. and Pal , D. 2001 . The interrelationships of side-chain and main-chain conformations in proteins . Progress in Biophysics and Molecular Biology , 76 : 1 – 102 .
   PubMed Web of Science ®Google Scholar
• Chothia , C. , Levitt , M. and Richardson , D. 1981 . Helix to helix packing in proteins . Journal of Molecular Biology , 145 : 215 – 250 .
   PubMed Web of Science ®Google Scholar
• Christopher , J.A. , Swanson , R. and Baldwin , T.O. 1996 . Algorithms for finding the axis of a helix: Fast rotational and parametric least-squares methods . Computers & Chemistry , 20 : 339 – 345 .
   PubMedGoogle Scholar
• Deupi , X. , Olivella , M. , Govaerts , C. , Ballesteros , J.A. , Campillo , M. and Pardo , L. 2004 . Ser and Thr residues modulate the conformation of pro-kinked transmembrane alpha-helices . Biophysical Journal , 86 : 105 – 115 .
   PubMed Web of Science ®Google Scholar
• Enkhbayar , P. , Damdinsuren , S. , Osaki , M. and Matsushima , N. 2008 . HELFIT: Helix fitting by a total least squares method . Computational Biology and Chemistry , 32 : 307 – 310 .
   PubMed Web of Science ®Google Scholar
• Frishman , D. and Argos , P. 1995 . Knowledge-based protein secondary structure assignment . Proteins , 23 : 566 – 579 .
   PubMed Web of Science ®Google Scholar
• Kabsch , W. and Sander , C. 1983 . Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features . Biopolymers , 22 : 2577 – 2637 .
   PubMed Web of Science ®Google Scholar
• Kahn , P.C. 1989 . Defining the axis of a helix . Computers & Chemistry , 13 : 185 – 189 .
   Google Scholar
• Kendrew , J.C. , Bodo , G. , Dintzis , H.M. , Parrish , R.G. , Wyckoff , H. and Phillips , D.C. 1958 . A three-dimensional model of the myoglobin molecule obtained by x-ray analysis . Nature , 181 : 662 – 666 .
   PubMed Web of Science ®Google Scholar
• Kumar, S. (1997). Geometry and sequence correlation studies on alpha-helices in globular protein. (Doctoral dissertation). Retrieved from JRD Tata Memorial Library, IISc. (G14762.).
   Google Scholar
• Kumar , S. and Bansal , M. 1996 . Structural and sequence characteristics of long alpha helices in globular proteins . Biophysical Journal , 71 : 1574 – 1586 .
   PubMed Web of Science ®Google Scholar
• Kumar , S. and Bansal , M. 1998 . Geometrical and sequence characteristics of alpha-helices in globular proteins . Biophysical Journal , 75 : 1935 – 1944 .
   PubMed Web of Science ®Google Scholar
• Langelaan , D.N. , Wieczorek , M. , Blouin , C. and 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 .
   PubMed Web of Science ®Google Scholar
• Love , W.E. , Klock , P.A. , Lattman , E.E. , Padlan , E.A. , Ward , K.B. Jr. and Hendrickson , W.A. 1972 . The structures of lamprey and bloodworm hemoglobins in relation to their evolution and function . Cold Spring Harbor Symposia on Quantitative Biology , 36 : 349 – 357 .
   PubMedGoogle Scholar
• MacArthur , M.W. and Thornton , J.M. 1996 . Deviations from planarity of the peptide bond in peptides and proteins . Journal of Molecular Biology , 264 : 1180 – 1195 .
   PubMed Web of Science ®Google Scholar
• McDonald , I.K. and Thornton , J.M. 1994 . Satisfying hydrogen bonding potential in proteins . Journal of Molecular Biology , 238 : 777 – 793 .
   PubMed Web of Science ®Google Scholar
• Mezei , M. and 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 .
   PubMed Web of Science ®Google Scholar
• Momany , F.A. , McGuire , R.F. , Burgess , A.W. and 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 .
   Web of Science ®Google Scholar
• Pauling , L. , Corey , R.B. and Branson , H.R. 1951 . The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain . Proceedings of the National Academy of Sciences of the United States of America , 37 : 205 – 211 .
   PubMed Web of Science ®Google Scholar
• Sankararamakrishnan , R. and Vishveshwara , S. 1990 . Conformational studies on peptides with proline in the right-handed alpha-helical region . Biopolymers , 30 : 287 – 298 .
   PubMed Web of Science ®Google Scholar
• Sankararamakrishnan , R. and Vishveshwara , S. 1992 . Geometry of proline-containing alpha-helices in proteins . International Journal of Peptide and Protein Research , 39 : 356 – 363 .
   PubMedGoogle Scholar
• Shakarji , C.M. 1998 . Least-squares fitting algorithms of the NIST algorithm testing system . Journal of Research of the National Institute of Standards and Technology , 103 : 633 – 641 .
   PubMed Web of Science ®Google Scholar
• Sugeta , H. and 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 .
   Web of Science ®Google Scholar
• Tusnady , G.E. , Dosztanyi , Z. and Simon , I. 2005a . PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank . Nucleic Acids Research , 33 : D275 – 278 .
   PubMed Web of Science ®Google Scholar
• Tusnady , G.E. , Dosztanyi , Z. and Simon , I. 2005b . TMDET: Web server for detecting transmembrane regions of proteins by using their 3D coordinates . Bioinformatics , 21 : 1276 – 1277 .
   PubMed Web of Science ®Google Scholar
• Visiers , I. , Braunheim , B.B. and Weinstein , H. 2000 . Prokink: A protocol for numerical evaluation of helix distortions by proline . Protein Engineering , 13 : 603 – 606 .
   PubMedGoogle Scholar
• Yohannan , S. , Faham , S. , Yang , D. , Whitelegge , J.P. and Bowie , J.U. 2004 . The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors . Proceedings of the National Academy of Sciences of the United States of America , 101 : 959 – 963 .
   PubMed Web of Science ®Google Scholar