Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 15215443

Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.

Andrew E Torda·James B Procter·Thomas Huber
View original source ↗Export metadata ↓

Abstract

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

Explore related subjects

Amino Acid SubstitutionInternetModels, MolecularProtein ConformationSequence Analysis, ProteinSoftwareUser-Computer InterfaceJournal Article

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Andrew E Torda, James B Procter, Thomas Huber. 2004-07-01. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.. https://doi.org/10.1093/nar%2Fgkh357

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

A new assay for nitric oxide reductase reveals two conserved glutamate residues form the entrance to a proton-conducting channel in the bacterial enzyme.

A specific amperometric assay was developed for the membrane-bound NOR [NO (nitric oxide) reductase] from the model denitrifying bacterium Paracoccus denitrificans using its natural electron donor, pseudoazurin, as a co-substrate. The method allows the rapid and specific assay of NO reduction catalysed by recombinant NOR expressed in the cytoplasmic membranes of Escherichia coli. The effect on enzyme activity of substituting alanine, aspartate or glutamine for two highly conserved glutamate residues, which lie in a periplasmic facing loop between transmembrane helices III and IV in the catalytic subunit of NOR, was determined using this method. Three of the substitutions (E122A, E125A and E125D) lead to an almost complete loss of NOR activity. Some activity is retained when either Glu122 or Glu125 is substituted with a glutamine residue, but only replacement of Glu122 with an aspartate residue retains a high level of activity. These results are interpreted in terms of these residues forming the mouth of a channel that conducts substrate protons to the active site of NOR during turnover. This channel is also likely to be that responsible in the coupling of proton movement to electron transfer during the oxidation of fully reduced NOR with oxygen [U. Flock, N. J. Watmough and P. Adelroth (2005) Biochemistry 44, 10711-10719].

Amino Acid Substitution↗
PubMed2007

Identification of JAK2V617F in patients with polycythemia is highly correlated with conventional criteria for diagnosis of polycythemia vera.

One hundred and forty four patients with a clinical indication of suspected polycythemia vera (PV), essential thrombocythemia, or idiopathic myelofibrosis were screened for JAK2(V617F) and the mutation frequency was 47, 51, and 50%, respectively. Previous investigations enabled 42 of 66 patients with suspected PV to be definitively diagnosed either as PV according to WHO criteria or to have this diagnosis excluded. Ninety-six percent of those with PV were JAK2(V617F), whereas all patients without PV did not have the mutation. Early screening of suspected PV patients for JAK2(V617F) rapidly identifies nearly all those with PV without invasive or less specific conventional investigations.

Amino Acid Substitution↗
PubMed2007

Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants.

The bacterial porin OmpF found in the outer membrane of E. coli is a wide channel, characterized by its poor selectivity and almost no ion specificity. It has an asymmetric structure, with relatively large entrances and a narrow constriction. By applying continuum electrostatic methods we determine the ionization states of titratable amino acid residues in the protein and calculate self-consistently the electric potential 3-D distribution within the channel. The average electrostatic properties are then represented by an effective fixed charge distribution along the pore which is the input for a macroscopic electrodiffusion model. The theoretical predictions agree with measurements performed under different salt gradients and pH. The sensitivity of reversal potential and conductance to the direction of the salt gradient and the solution pH is captured by the model. The theory is also able to explain the influence of the lipid membrane charge. The same methodology is satisfactorily applied to some OmpF mutants involving slight structural changes but a large number of net charges. The correlation found between atomic structure and ionic selectivity shows that the transport characteristics of wide channels like OmpF and its mutants are mainly regulated by the collective action of a large number of residues, rather than by the specific interactions of residues at particular locations.

Amino Acid Substitution↗