Dataset Information

STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

ABSTRACT: STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Calpha-Calpha and Cbeta-Cbeta distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)-amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS.

SUBMITTER: Neshich G

PROVIDER: S-EPMC168984 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature

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STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Neshich Goran G Togawa Roberto C RC Mancini Adauto L AL Kuser Paula R PR Yamagishi Michel E B ME Pappas Georgios G Torres Wellington V WV Fonseca e Campos Tharsis T Ferreira Leonardo L LL Luna Fabio M FM Oliveira Adilton G AG Miura Ronald T RT Inoue Marcus K MK Horita Luiz G LG de Souza Dimas F DF Dominiquini Fabiana F Alvaro Alexandre A Lima Cleber S CS Ogawa Fabio O FO Gomes Gabriel B GB Palandrani Juliana F JF dos Santos Gabriela F GF de Freitas Esther M EM Mattiuz Amanda R AR Costa Ivan C IC de Almeida Celso L CL Souza Savio S Baudet Christian C Higa Roberto H RH

Nucleic acids research 20030701 13

STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web i ...[more]

PMID: 12824333

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Project description:BackgroundThe 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.ResultsWe 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.ConclusionSMS 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.

Project description:BackgroundAccurately modeling the sequence substitution process is required for the correct estimation of evolutionary parameters, be they phylogenetic relationships, substitution rates or ancestral states; it is also crucial to simulate realistic data sets. Such simulation procedures are needed to estimate the null-distribution of complex statistics, an approach referred to as parametric bootstrapping, and are also used to test the quality of phylogenetic reconstruction programs. It has often been observed that homologous sequences can vary widely in their nucleotide or amino-acid compositions, revealing that sequence evolution has changed importantly among lineages, and may therefore be most appropriately approached through non-homogeneous models. Several programs implementing such models have been developed, but they are limited in their possibilities: only a few particular models are available for likelihood optimization, and data sets cannot be easily generated using the resulting estimated parameters.ResultsWe hereby present a general implementation of non-homogeneous models of substitutions. It is available as dedicated classes in the Bio++ libraries and can hence be used in any C++ program. Two programs that use these classes are also presented. The first one, Bio++ Maximum Likelihood (BppML), estimates parameters of any non-homogeneous model and the second one, Bio++ Sequence Generator (BppSeqGen), simulates the evolution of sequences from these models. These programs allow the user to describe non-homogeneous models through a property file with a simple yet powerful syntax, without any programming required.ConclusionWe show that the general implementation introduced here can accommodate virtually any type of non-homogeneous models of sequence evolution, including heterotachous ones, while being computer efficient. We furthermore illustrate the use of such general models for parametric bootstrapping, using tests of non-homogeneity applied to an already published ribosomal RNA data set.

Project description:BackgroundThe number of people living with dementia is increasing worldwide, mainly because of aging of the population. To date, there is no pharmaceutical intervention to delay or treat cognitive decline or dementia. As an estimated one-third of dementia cases might be attributable to modifiable lifestyle factors (such as cognitive and physical activity), multidomain lifestyle interventions are a promising way to maintain or improve brain health. Offering programs online would enable large-scale implementation. An overview of multidomain Web-based lifestyle programs for brain health would facilitate comparison and improvement of such programs to develop effective and sustainable interventions.ObjectiveThis study aimed to (1) provide a comprehensive overview of Web-based multidomain lifestyle programs aimed at optimizing brain health in healthy adult populations and (2) describe the programs and targeted lifestyle factors, availability, and evaluation of adherence and user experience. In addition, a meta-analysis was performed to evaluate the effectiveness of these programs.MethodsElectronic databases (PubMed, EMBASE, and PsycINFO) were searched for Web-based lifestyle programs that were included when the program (1) aimed to optimize brain health, (2) focused on multiple lifestyle factors, (3) was completely Web-based (website, Web application or mobile app), (4) consisted of multiple sessions, and (5) focused on a healthy adult population. Program characteristics (target population, duration, frequency, tailoring, platform, and availability) and results of program evaluations (effectiveness, user evaluations, and adherence) were extracted and compared. Studies using a controlled design were included in a random-effects meta-analysis on the effectiveness on brain health outcomes. Study quality was assessed using the physiotherapy evidence database (PEDro) scale.ResultsThe electronic searches yielded 44 documents describing 14 Web-based lifestyle programs; physical and cognitive activities were targeted in all programs. Four programs (4/14, 29%) were publicly available and free of charge, whereas others were restricted to research settings (5/14, 36%), available after payment (1/14, 7%), or not available at all (2/14, 14%). User evaluations were reported for 8 (57%) of the 14 programs. Reported dropout of the intervention groups ranged from 2% to 52%. Overall, 3 studies evaluated the effectiveness of a program using a controlled design and were included in the meta-analysis (moderate-to-high quality). Pooled results showed a significant small-to-medium effect of the Web-based multidomain lifestyle interventions on outcome measures for brain health (global cognition score, subjective cognitive score, and lifestyle risk score; standard mean difference=0.45; 95% CI 0.12-0.78), with a high degree heterogeneity across studies (I2=75%; P=.02).ConclusionsIn total, 14 Web-based multidomain lifestyle programs aimed at optimizing brain health were found. The programs showed heterogeneity in both characteristics and effectiveness evaluation. Despite this heterogeneity, this meta-analysis suggests that Web-based lifestyle programs can positively influence brain health outcomes and have the potential to contribute to the prevention of dementia.

Dataset Information

STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Publications

STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

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