STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Abstract

Background: The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.

Results: We are reporting here about new Sting Millennium Suite (SMS) version which is fully accessible (including for local files at client end), web based software for molecular structure and sequence/structure/function analysis. The new SMS client version is now operational also on Linux boxes and it works with non-public pdb formatted files (structures not deposited at the RCSB/PDB), eliminating earlier requirement for the registration if SMS components were to be used with user's local files. At the same time the new SMS offers some important additions and improvements such as link to ProTherm as well as significant re-engineering of SMS component ConSSeq. Also, we have added 3 new SMS mirror sites to existing network of global SMS servers: Argentina, Japan and Spain.

Conclusion: SMS is already established software package and many key data base and software servers worldwide, do offer either a link to, or host the SMS. SMS (Sting Millennium Suite) is web-based publicly available software developed to aid researches in their quest for translating information about the structures of macromolecules into knowledge. SMS allows to a user to interactively analyze molecular structures, cross-referencing visualized information with a correlated one, available across the internet. SMS is already used as a didactic tool by some universities. SMS analysis is now possible on Linux OS boxes and with no requirement for registration when using local files.

Figure 1

SMS sequence and structure window. This SMS example screen displays the pdb file 1cho.pdb, highlighting the residue Leu46 in chain E. SMS sequence frame, from where all the SMS modules and features can be accessed, is shown at the top of this figure. The sequence is colored according to physical-chemical properties of the amino acids. The blue and red lines underneath the amino acid sequence represent the secondary structure elements (beta strands and helices respectively), according to the pdb file annotation. As the user scrolls the mouse over the sequence, information about the residues appears in the "residue info" box. Pull-down menu on the top of the sequence frame is also shown, demonstrating choice of SMS modules and rendering. SMS structure frame (Chime wiondow) is shown at the bottom of this figure. This figure was centered on the Leu_46 (painted in red) of the E chain. The other residues drawn in stick presentation are the residues that make contacts with the Leucine, colored according to the contacts they make, corresponding to the first two lines of the Protein Dossier in Figure 2.

Figure 2

SMS Protein Dossier. Protein Dossier module – The meaning of the colors are on the top part of the image. The internal and interface forming contacts are shown above the amino acid sequence cartoon, color coded according to the type of contact. The first row (red line) under the sequence highlights the residues at the interface. The next row (yellow line bellow the sequence stretch: VTAAHGC) indicates the PROSITE pattern PS00134. The following three rows indicate the secondary structure according to the annotations in PDB, DSSP and Stride, respectively. Another five rows are displayed color coded according to: temperature factor, relative entropy, accessibility in complex, accessibility in isolation and dihedral angles.

Figure 3

Atomic contacts among residues within same chain. Internal residue contacts formed by the Leu_46, showing all amino acids, belonging to the same chain E, that make contacts with it. The fan above the residue is color coded according to the type of contact the residue is involved with.

Figure 4

Sequence Conservation in SMS ConSSeq. ConSSeq window where the amino acid sequence of 1cho, chain E is aligned with a consensus sequence as found in HSSP and, entropy histogram color and size coded with respect to the calculated degree of conservation. The size of sequence letters in the "logo" follows the same degree of conservation, while color coding is the same as in SMS sequence frame. Leu_46 is highlighted by sequence number 46 colored red.

Figure 5

SMS Ramachandran interactive plot. Ramachandran plot of 1cho.pdb, highlighting the position of Leu_46 (blue colored spot), chain E in the diagram, and coloring plotted areas according to the allowed regions for the phi and psi angles. This image shows also the area of the applet which is dedicated to sub setting of the amino acids according to their type and position in the allowed and disallowed areas.