SIR99, a program for the automatic solution of small and large crystal structures

1999 ◽  
Vol 55 (6) ◽  
pp. 991-999 ◽  
Author(s):  
Maria Cristina Burla ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Ab Initio ◽  
Crystal Structures ◽  
Prior Information ◽  
Flow Diagram ◽  
Large Crystal ◽  
Large Molecules ◽  
Small Proteins ◽  
Practical Information ◽  
User Intervention

The moduli and flow diagram of the program SIR99 are described. New phasing algorithms are proposed working both in direct and in reciprocal space. Their cooperative work is able to solve the structures of both small and large molecules. In particular, small proteins can be solved ab initio without any use of prior information and any user intervention. The efficiency of the various algorithms employed by SIR99 has been tested, and the role of the tangent formula clarified. The user is also provided with some practical information concerning the computer power needed.

SIR2000-N, a program for large and small crystal structures

2001 ◽  
Vol 34 (4) ◽  
pp. 523-526 ◽  
Author(s):  
Maria Cristina Burla ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Ab Initio ◽  
Small Molecules ◽  
Crystal Structures ◽  
Acta Cryst ◽  
Small Crystal ◽  
Data Resolution

The programSIR2000[Burlaet al.(2000).Acta Cryst.A56, 451–457] was designed for theab initiosolution of macromolecular crystal structures, provided that the data resolution is no lower than 1.2 Å. As the phasing procedure ofSIR2000is rather time consuming, modifications have been introduced to improve its efficiency and to make it additionally suitable for small molecules (new versionSIR2000-N). The role of the tangent refinement in modern phasing procedures is enlightened.

Solving Crystal Structures from Powder Data. I. The Role of the Prior Information in the Two-Stage Method

1996 ◽  
Vol 29 (6) ◽  
pp. 667-673 ◽  
Author(s):  
A. Altomare ◽  
B. Carrozzini ◽  
C. Giacovazzo ◽  
A. Guagliardi ◽  
A. G. G. Moliterni ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Prior Information ◽  
Two Stage

SIR88 – a direct-methods program for the automatic solution of crystal structures

1989 ◽  
Vol 22 (4) ◽  
pp. 389-393 ◽  
Author(s):  
M. C. Burla ◽  
M. Camalli ◽  
G. Cascarano ◽  
C. Giacovazzo ◽  
G. Polidori ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Phase Structure ◽  
Prior Information ◽  
Direct Methods ◽  
Partial Structure ◽  
Two Phase ◽  
Acta Cryst ◽  
Space Groups ◽  
Structure Solution ◽  
User Intervention

SIR88 is an integrated package of computer programs for the solution of crystal structures. The package is based on the estimation of one- and two-phase structure seminvariants and three- and four-phase structure invariants according to the theory of representations [Giacovazzo (1977). Acta Cryst. A33, 933–944; (1980). Acta Cryst. A36, 362–372]. The program works in all the space groups and in most cases it is able to provide the correct solution without user intervention. Some prior information like the availability of a partial structure or of pseudotranslational symmetry is easily exploited to obtain the structure solution.

scholarly journals AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computedab initiomodels

2012 ◽  
Vol 68 (12) ◽  
pp. 1622-1631 ◽  
Author(s):  
Jaclyn Bibby ◽  
Ronan M. Keegan ◽  
Olga Mayans ◽  
Martyn D. Winn ◽  
Daniel J. Rigden
Keyword(s):  
Ab Initio ◽  
Crystal Structures ◽  
Sequence Data ◽  
Data File ◽  
Test Cases ◽  
Molecular Replacement ◽  
Computational Pipeline ◽  
Small Proteins ◽  
Sequence File ◽  
Local Accuracy

Proteinab initiomodels predicted from sequence data alone can enable the elucidation of crystal structures by molecular replacement. However, the calculation of suchab initiomodels is typically computationally expensive. Here, a computational pipeline based on the clustering and truncation of cheaply obtainedab initiomodels for the preparation of structure ensembles is described. Clustering is used to select models and to quantitatively predict their local accuracy, allowing rational truncation of predicted inaccurate regions. The resulting ensembles, with or without rapidly added side chains, solved 43% of all test cases, with an 80% success rate for all-α proteins. A program implementing this approach,AMPLE, is included in theCCP4 suite of programs. It only requires the input of aFASTAsequence file and a diffraction data file. It carries out the modelling using locally installedRosetta, creates search ensembles and automatically performs molecular replacement and model rebuilding.

The role of density reduction in lithiated amorphous silicon: Molecular dynamics and ab-initio studies

2021 ◽  
Author(s):  
Jay Krishan Dora ◽  
Charchit Saraswat ◽  
Ashish Gour ◽  
Sudipto Ghosh ◽  
Natraj Yedla ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Amorphous Silicon ◽  
Density Reduction

scholarly journals 332 The diagnostic role of shunt series radiographs (SSR) in children presenting to the children’s emergency department (CED) with suspected ventriculoperitoneal (VP) shunt failure

2020 ◽  
Vol 37 (12) ◽  
pp. 852.3-853
Author(s):  
Angharad Griffiths ◽  
Ikechukwu Okafor ◽  
Thomas Beattie
Keyword(s):  
Clinical Outcome ◽  
Sensitivity And Specificity ◽  
Clinical Information ◽  
Flow Diagram ◽  
List Type ◽  
Shunt Failure ◽  
Vp Shunt ◽  
Wide Range ◽  
Diagnostic Role

Aims/Objectives/BackgroundVP shunts are used to drain CSF from the cranial vault because of a wide range of pathologies and, like any piece of hardware, can fail. Traditionally investigations include SSR and CT. This project examines the role of SSR in evaluating children with suspected VP shunt failure.Primary outcome: Sensitivity and specificity of SSR in children presenting to the CED with concern for shunt failure.Methods/DesignConducted in a single centre, tertiary CED of the national Irish Neurosurgical(NS) referral centre (ED attendance:>50,000 patients/year). 100 sequential SSR requested by the CED were reviewed. Clinical information was extracted from electronic requests. Shunt failure was defined by the need for NS intervention(Revision).Abstract 332 Figure 1Abstract 332 Figure 2Results/ConclusionsSensitivity and specificity is presented in figure 1 (two by two table).100 radiographs performed in 84 children.22% shunts revised (see flow diagram).7 SSR’s were abnormal.85% (n=6) shunts revised. [5 following abnormal CT].Of the normal SSR’s; 16 had abnormal CT and revised.85/100 received CT.64 of 85 CT’s (75%) were normal.□6 of the 64 had focal shunt concern.SSR’s shouldn’t be used in isolation. NPV&PPV, Sensitivity&Specificity is low.SSR’s are beneficial where there’s concern over focal shunt problems (injury/pain/swelling) or following abnormal CT.VP shunt failure is not well investigated with SSR alone.SSR’s could be omitted where there is no focal shunt concern/after normal CT (without impacting clinical outcome) reducing radiation exposure and reduce impact on CED’s.59 SSR’s could have been avoided without adverse clinical outcome.

scholarly journals Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation

2021 ◽  
Vol 9 (5) ◽  
pp. 1046
Author(s):  
Inam Ul Haq ◽  
Sabine Brantl
Keyword(s):  
Bacillus Subtilis ◽  
Antisense Rna ◽  
Rna Binding ◽  
Rna Degradation ◽  
Metabolic Enzyme ◽  
Dual Function ◽  
Small Proteins ◽  
Moonlighting Proteins ◽  
Rnase Y

Moonlighting proteins are proteins with more than one function. During the past 25 years, they have been found to be rather widespread in bacteria. In Bacillus subtilis, moonlighting has been disclosed to occur via DNA, protein or RNA binding or protein phosphorylation. In addition, two metabolic enzymes, enolase and phosphofructokinase, were localized in the degradosome-like network (DLN) where they were thought to be scaffolding components. The DLN comprises the major endoribonuclease RNase Y, 3′-5′ exoribonuclease PnpA, endo/5′-3′ exoribonucleases J1/J2 and helicase CshA. We have ascertained that the metabolic enzyme GapA is an additional component of the DLN. In addition, we identified two small proteins that bind scaffolding components of the degradosome: SR1P encoded by the dual-function sRNA SR1 binds GapA, promotes the GapA-RNase J1 interaction and increases the RNase J1 activity. SR7P encoded by the dual-function antisense RNA SR7 binds to enolase thereby enhancing the enzymatic activity of enolase bound RNase Y. We discuss the role of small proteins in modulating the activity of two moonlighting proteins.

scholarly journals Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannes Petruschke ◽  
Christian Schori ◽  
Sebastian Canzler ◽  
Sarah Riesbeck ◽  
Anja Poehlein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Microbiota ◽  
De Novo ◽  
Bacterial Species ◽  
Intestinal Microbiome ◽  
Single Strain ◽  
Small Proteins ◽  
Human Intestinal Microbiota ◽  
Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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