supp - Springer Static Content Server
... HnRNP F is an RNA binding protein belonging to the HnRNP H protein family that contains four highly homologous members, namely HnRNP H, HnRNP H’, HnRNP F, and HnRNP 2H9. These proteins contain two (2H9) or three (H, H’, and F) RNA recognition motifs (RRM) and two glycine rich auxiliary domains (Hono ...
... HnRNP F is an RNA binding protein belonging to the HnRNP H protein family that contains four highly homologous members, namely HnRNP H, HnRNP H’, HnRNP F, and HnRNP 2H9. These proteins contain two (2H9) or three (H, H’, and F) RNA recognition motifs (RRM) and two glycine rich auxiliary domains (Hono ...
Supplementary Information (doc 42K)
... 1 symbiont, the Riftia 2 symbiont and the Tevnia symbiont. Asterisk: Protein is also involved ...
... 1 symbiont, the Riftia 2 symbiont and the Tevnia symbiont. Asterisk: Protein is also involved ...
Click for format template in MS Word file
... Results: This study used 2,746 WNV protein sequences collected from the NCBI GenPept database, and focused on analyzing peptides of length 9 amino acids or more, immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences revealed the presence of n ...
... Results: This study used 2,746 WNV protein sequences collected from the NCBI GenPept database, and focused on analyzing peptides of length 9 amino acids or more, immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences revealed the presence of n ...
What is function
... • should be able to give reliable statistics • do we like them ? • fundamental problem • difficult to see how characteristic a pattern is • not a causal relationship • structural versus local sequence properties… ...
... • should be able to give reliable statistics • do we like them ? • fundamental problem • difficult to see how characteristic a pattern is • not a causal relationship • structural versus local sequence properties… ...
Structural model and prop of the AdolVletDC of
... bifunctional S-adenosylmethionine decar boxy lase / Orni thine decar boxy lase (AdoMetD C/ O D C) enzyme, represents one such target. Within this enzyme reside the two main regulatory activities for the biosyn thesis of polyamines. Furthermore, the bifunctional arrangement does not occur in the hum ...
... bifunctional S-adenosylmethionine decar boxy lase / Orni thine decar boxy lase (AdoMetD C/ O D C) enzyme, represents one such target. Within this enzyme reside the two main regulatory activities for the biosyn thesis of polyamines. Furthermore, the bifunctional arrangement does not occur in the hum ...
Is β-pleated sheet the molecular conformation which dictates
... proteins producing results in good agreement with experimental data, where individual prediction methods usually fail to produce meaningful results (Hamodrakas et al., 1982a; Hamodrakas and Kafatos, 1984; Hamodrakas, 1992). 2.2. Cuticular proteins The 27 proteins chosen for inclusion in this analysi ...
... proteins producing results in good agreement with experimental data, where individual prediction methods usually fail to produce meaningful results (Hamodrakas et al., 1982a; Hamodrakas and Kafatos, 1984; Hamodrakas, 1992). 2.2. Cuticular proteins The 27 proteins chosen for inclusion in this analysi ...
preprint - Human Genome Center
... Note that E(i, j, ℓ) is the G(i, i + ℓ − 1) for the range RMSD query problem between P[1..n′′ ] and Q[j − i + 1..n′′ + j − i], where n′′ = min(n, m − j + i). As for ⃗hP (i, i + ℓ − 1), ⃗hQ (j, j + ℓ − 1), h2P (i, i + ℓ − 1) and h2Q (j, j + ℓ − 1), they can be computed in constant time after linear t ...
... Note that E(i, j, ℓ) is the G(i, i + ℓ − 1) for the range RMSD query problem between P[1..n′′ ] and Q[j − i + 1..n′′ + j − i], where n′′ = min(n, m − j + i). As for ⃗hP (i, i + ℓ − 1), ⃗hQ (j, j + ℓ − 1), h2P (i, i + ℓ − 1) and h2Q (j, j + ℓ − 1), they can be computed in constant time after linear t ...
Effect of Structural Changes in Proteins Derived from GATA4
... Manjegowda, et al.: Role of nsSNPs of GATA4 in Manifestation of CHD Congenital heart disease is the most common type of birth defect. The single nucleotide polymorphism in GATA4 is associated with various congenital heart disease phenotypes. In the present study, we analysed the nonsynonymous single ...
... Manjegowda, et al.: Role of nsSNPs of GATA4 in Manifestation of CHD Congenital heart disease is the most common type of birth defect. The single nucleotide polymorphism in GATA4 is associated with various congenital heart disease phenotypes. In the present study, we analysed the nonsynonymous single ...
The Endoplasmic Reticulum Glucosyltransferase
... only element of the mechanism that senses glycoprotein conformational states. This quality control mechanism is not the only one operating in the ER as there are alternative mechanisms for retaining proteins not displaying their fully folded structures, as those involving other conventional chaperon ...
... only element of the mechanism that senses glycoprotein conformational states. This quality control mechanism is not the only one operating in the ER as there are alternative mechanisms for retaining proteins not displaying their fully folded structures, as those involving other conventional chaperon ...
Distributed Representations for Biological Sequence Analysis
... Apart from this encouraging performance on the protein classification task, a word embeddings based approach offers other advantages. First, the size of the data vector obtained by using embeddings is much smaller in comparison to the original sequence, thus making the vectors obtained amenable for ...
... Apart from this encouraging performance on the protein classification task, a word embeddings based approach offers other advantages. First, the size of the data vector obtained by using embeddings is much smaller in comparison to the original sequence, thus making the vectors obtained amenable for ...
The Three Dimensional Structure of Proteins
... The folding of a single polypeptide chain in three dimensional space is Tertiary Structure. Tertiary structures involves long range interactions within the polypeptide. The protein folds upon itself resulting in a tight compact shape, a conformation, that is at an energy minimum and an entropy maxim ...
... The folding of a single polypeptide chain in three dimensional space is Tertiary Structure. Tertiary structures involves long range interactions within the polypeptide. The protein folds upon itself resulting in a tight compact shape, a conformation, that is at an energy minimum and an entropy maxim ...
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen
... • Align human genome 100 bp read dataset with 30fold coverage in 20 minutes on a 32-core server ...
... • Align human genome 100 bp read dataset with 30fold coverage in 20 minutes on a 32-core server ...
Publication: Sequence Analysis of Holins by Reduced Amino Acid
... Holins are small membrane proteins responsible for disrupting the cytoplasmic membrane of bacteria to release endolysins which hydrolyze the cell wall and induce cell death [1]. The holin genes are encoded in the genome of bacteriophages to mainly control the phage infection cycle. These genes play ...
... Holins are small membrane proteins responsible for disrupting the cytoplasmic membrane of bacteria to release endolysins which hydrolyze the cell wall and induce cell death [1]. The holin genes are encoded in the genome of bacteriophages to mainly control the phage infection cycle. These genes play ...
Poly(Pro)II Helices in Globular Proteins: Identification and Circular
... single residue in the PIIconformation cannot be considered as a PIIhelix, but even in an isolated PIIresidue two successive amide groups are oriented so that the exciton interaction expected in a PIIhelix is possible. We evaluated both these possibilities by considering all residues in PIIstructure ...
... single residue in the PIIconformation cannot be considered as a PIIhelix, but even in an isolated PIIresidue two successive amide groups are oriented so that the exciton interaction expected in a PIIhelix is possible. We evaluated both these possibilities by considering all residues in PIIstructure ...
No Slide Title
... if these hydrogen bonded amides match with regions that we identified previously as a-helices, b-sheets, or b-turns. • If we can do this, then, and ONLY then, we can use a H-bond constraint during the generation of our 3D model. • Why the ONLY? We only now the H-bond donor, but there is (or there wa ...
... if these hydrogen bonded amides match with regions that we identified previously as a-helices, b-sheets, or b-turns. • If we can do this, then, and ONLY then, we can use a H-bond constraint during the generation of our 3D model. • Why the ONLY? We only now the H-bond donor, but there is (or there wa ...
Ammonia-Nitrogen in Fermented Feeds - Agri
... Ammonia-N in silage is produced by the breakdown of protein by either plant proteolytic enzymes, or clostridial microorganisms (secondary fermentation). Although NH 3-N is not considered as protein (Nonprotein nitrogen-NPN), it provides N that can be used by rumen bacteria to synthesize microbial pr ...
... Ammonia-N in silage is produced by the breakdown of protein by either plant proteolytic enzymes, or clostridial microorganisms (secondary fermentation). Although NH 3-N is not considered as protein (Nonprotein nitrogen-NPN), it provides N that can be used by rumen bacteria to synthesize microbial pr ...
Protein Structure and Function
... Ab initio method - Equilibrium conformation is the global free-energy minimum - potential energy parameter is accurate (H-bond, van der Waals etc) - key intermediates? - oligomerization can not be addressed although very many globular proteins are oligomeric. ...
... Ab initio method - Equilibrium conformation is the global free-energy minimum - potential energy parameter is accurate (H-bond, van der Waals etc) - key intermediates? - oligomerization can not be addressed although very many globular proteins are oligomeric. ...
Crystal structure of ICE and Protein
... - There are also two metastable phases of ice under pressure, both fully hydrogen disordered: IV and XII. Ices XI, XIII, and XIV are hydrogen-ordered forms of ices Ih, V, and XII ...
... - There are also two metastable phases of ice under pressure, both fully hydrogen disordered: IV and XII. Ices XI, XIII, and XIV are hydrogen-ordered forms of ices Ih, V, and XII ...
Bioinfo primer - part 4/6
... nature and frequencies of the amino acids, and cover a larger range of values. ...
... nature and frequencies of the amino acids, and cover a larger range of values. ...
Database searching with DNA and protein sequences
... replacing them by the character X, using, for example, the program SEG.17 ...
... replacing them by the character X, using, for example, the program SEG.17 ...
Enantiomers and Diastereomers File
... Another type of geometric isomer is found in ring structures and doesn’t involve double bonds Due to the inflexible nature of the bonds that make up the ring Note: The ring lies on a flat plane (e.g. your paper) and the OH groups are perpendicular to the plane (e.g. up and down) ...
... Another type of geometric isomer is found in ring structures and doesn’t involve double bonds Due to the inflexible nature of the bonds that make up the ring Note: The ring lies on a flat plane (e.g. your paper) and the OH groups are perpendicular to the plane (e.g. up and down) ...
a version - SEA
... Superfamilies I, II and III may be present, but we have found no evidence for holins from Superfamilies V and VI in these phages. The strongest motif in Superfamily VII proteins aligns with cytoplasmic amino acids directly upstream of a transmembrane helix, indicating that these motifs may correspon ...
... Superfamilies I, II and III may be present, but we have found no evidence for holins from Superfamilies V and VI in these phages. The strongest motif in Superfamily VII proteins aligns with cytoplasmic amino acids directly upstream of a transmembrane helix, indicating that these motifs may correspon ...
File - prepareforchemistry
... sulphite addition product. However, glucose does not undergo these reactions. (2) The pentaacetate of glucose does not react with hydroxylamine. This indicates that a free −CHO group is absent from glucose. (3) Glucose exists in two crystalline forms − ∝ andβ. The ∝ -form (m.p. = 419 K) crystallises ...
... sulphite addition product. However, glucose does not undergo these reactions. (2) The pentaacetate of glucose does not react with hydroxylamine. This indicates that a free −CHO group is absent from glucose. (3) Glucose exists in two crystalline forms − ∝ andβ. The ∝ -form (m.p. = 419 K) crystallises ...
Sequence Data Analysis: A Bioinformatics Application
... Better Understand Protein Disorders Hypothesis: • Since amino acid sequence determines structure, sequence should determine lack of structure (disorder) as well. Test • Construct a protein disorder predictor • Check its accuracy • Apply it on large protein sequence databases ...
... Better Understand Protein Disorders Hypothesis: • Since amino acid sequence determines structure, sequence should determine lack of structure (disorder) as well. Test • Construct a protein disorder predictor • Check its accuracy • Apply it on large protein sequence databases ...
Proteins * Structure and Function
... The R group represents a side chain from the central ‘alpha’ carbon atom, and can be anything from a simple hydrogen atom to a more complex ring structure. 3 of 29 ...
... The R group represents a side chain from the central ‘alpha’ carbon atom, and can be anything from a simple hydrogen atom to a more complex ring structure. 3 of 29 ...
Structural alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.