2Struc: the secondary structure server

Abstract

Summary: The defined secondary structure of proteins method is often considered the gold standard for assignment of secondary structure from three-dimensional coordinates. However, there are alternative methods. ‘2Struc: The Secondary Structure Server’ has been created as a single point of access for eight different secondary structure assignment methods. It has been designed to enable comparisons between methods for analyzing the secondary structure content for a single protein. It also includes a second functionality, ‘Compare-the-Protein’ to enable comparisons of the secondary structure features from any one method to be made within a collection of nuclear magnetic resonance models, or between the crystal structures of two different proteins.Availability: http://2struc.cryst.bbk.ac.ukContact: r.w.janes@qmul.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

An Algorithm for Protein Helix Assignment Using Helix Geometry

“…On set ℕ our algorithm assigns 178,104 α -helices with a length from 4 to 212 residues and the most frequently appeared helix has a length of 10 residues; 70,208 3 10 -helices with a length from 3 to 14 residues with the most frequently appeared ones has a length of 3 residues; and finally 6,600 π -helices with a length from 5 to 18 residues and the most frequently appeared ones has a length of 5 residues. Due to the difficulty of obtaining a local copy for the programs palsse , stick , xtlsstr , kaksi and sst we have tested them on the set 𝕋 of 100 selected x-ray structures by uploading each one to a web server [23] to obtain their assignments (Table 4). The comparison with the program disicl is made on the same set 𝕋.…”

“…The set of the remaining 25,806 structures (set ℕ) is used to evaluate the performance of our algorithm and two previous programs dssp and stride . To compare our algorithm with the five programs ( kaksi , plasse , stick , stlsstr and sst ) that we are not able to obtain a local copy we have uploaded to a web server [23] a set of 100 x-ray protein structures (set 𝕋) with the first 50 structures having resolutions between 1.0Å–2.0Å and the rest having resolutions ≥ 2.5Å(1AKG,1BGF,1EZW,1GSU,1I1N,1K1B,1NTE,1O98,1PVM,1SJD,1UKF,1VZY,1XGW,1YQD,2ASC, 2BJI, 2CWH,2FD5,2GB2, 2GG6,2H1V,2I2C,2NSF, 2POK,2VBA,2W6K,2WRA,2X7H,2YSK,2ZJ3,3C9U,3EDF, 3GG7,3HG7,3IDV,3LCC,3LFJ,3P4H,3PUA, 3TOU,3V7Q,3ZOO;1AZ2,1BTN,1CAX,1F1F,1FXA,1HMY,1KX8, 1MJ9,1MSC,1NJ1,1PYP,1RIN,2CND,2GAE,2HAF,2HXB,2QQV, 2RJQ,2SPT,2WO7,2X2B,2Y5Q,2ZIY,3AT0, 3G0A,3IIA,3L1G,3M3T,3NPE,3O5K,3PGK,3PMQ,3QNT,3QYB,3T2Y,3UUF,3VGE, 3WMF,4AYH,4BOY, 4EWS,4GB0,4JVC,4LIF,4MBR,4N3G,4O1S,4PUT,4QGL,4TW8) to obtain their helix assignments. Set 𝕋 is also used for a comparison with the program disicl .…”

Parallel In-register Intermolecular β-Sheet Architectures for Prion-seeded Prion Protein (PrP) Amyloids

“…Models were analyzed, and images were created using VMD and UCSF Chimera. Secondary structure was analyzed with the DSSP algorithm (47).…”

Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability

“…Volume calculations were done using the server 3V: Voss Volume Voxelator [61], radius of gyration calculation of each protein structures was carried out using HYDROPRO utility [62]. Secondary structure contents were calculated using 2Struc server [63]. HBPLUS [64] was used for calculating hydrogen bonds (with donor-acceptor cut-off distance of 3.5Å and donor-hydrogen-acceptor angle to be at least 90 • ) and salt-bridges were detected using WHATIF server [65].…”