sequence-to-model alignments. Although DSMs are generally represented as hidden Markov models (HMMs), they are designed around a set of rules rather than trained on a large representative set, as most HMMs are. The DSM approach to protein structure modeling has many advantages: flexibility, generality, a high degree of abstraction, and the possibility to build models for hypothetical structures...

We describe a new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements. The library was generated using an automated method for finding correlations between protein sequence and local structure, and contains most previously described local sequence-structure correlations as well as n...

Likelihood estimates of local rates of evolution within proteins reveal that selective constraints on structure and function are quantitatively stable over billions of years of divergence. The stability of constraints produces an intramolecular clock that gives each protein a characteristic pattern of evolutionary rates along its sequence. This pattern allows the identification of constrained r...

background and objectives: during past decades hansenula polymorpha has attracted global attention for the expression of recombinant proteins due to its high growth rate, minimal nutritional porequirements and use of methanol as a low cost inducer. materials and methods: the corresponding nucleotide sequences for the expression of heterologous genes in hansenula poylmorpha were extracted and as...

Here, we present PatMatch, an efficient, web-based pattern-matching program that enables searches for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences. The program can be used to find matches to a user-specified sequence pattern that can be described using ambiguous sequence codes and a powerful and flexible patt...

Background: Denileukin diftitox (trade name, Ontak) is the first recombinant immunotoxin (IM), in which the binding domain of diphtheria toxin has been replaced by the amino acid sequence of human interleukin-2 (DT389IL-2) using genetic engineering. Purity, stability, and structural property of the protein are critical factors for the scale-up production of this fusion protein. In this IM, loca...

Abstract The acidic activation domain (AD) of yeast transcription factor Gal4 plays a dual role in repression and through binding to Gal80 repressor Mediator subunit Med15. function arises from two hydrophobic regions within the 40-residue AD. We show by NMR that each AD region binds Med15 using “fuzzy” protein interface. Remarkably, comparison chemical shift perturbations shows Gcn4, intrinsic...

Tomato yellow leaf curl virus (TYLCV) is a major devastating viral disease, majorly affecting the tomato production globally. The disease transmitted by Whitefly. Begomovirus having six protein coding genes, among them C1/AC1 evidently associated with replication. Owing to immense role of gene, present study an initial effort elucidate factors shaping codon usage bias and evolutionary pattern T...

Infectious bursal disease (IBD), a highly contagious and devastating disease in young chicken, is causedby infectious bursal disease virus (IBDV). To improve the immunogenicity of recombinant IBDV subunitvaccine, an attempt was made to find a new way to prepare IBD vaccine containing glycosylated mVP2antigen. Firstly, IBDV mVP2 gene (with a nucleic acid sequence encoding B cell epitope of IBDV(...