Predicting the sidechain dihedral angle distributions
... measured backbone and side-chain dihedral angle distributions using knowledge-based potentials, such as CHARMM-CMAP14 and v-CMAP,15 or AmberILDN.16 Thus, the molecular mechanics force fields do not allow one to quantify the distinct contribution of steric repulsive interactions to the side-chain dih ...
... measured backbone and side-chain dihedral angle distributions using knowledge-based potentials, such as CHARMM-CMAP14 and v-CMAP,15 or AmberILDN.16 Thus, the molecular mechanics force fields do not allow one to quantify the distinct contribution of steric repulsive interactions to the side-chain dih ...
tutorial_structurech..
... In the same way the usage information for any of the provided commands can be obtained. For example, typing cispeptide restrain will show the syntax of the command that generates restraints for the dihedral angle at the peptide bond which can be used in NAMD. In the following, we will describe how t ...
... In the same way the usage information for any of the provided commands can be obtained. For example, typing cispeptide restrain will show the syntax of the command that generates restraints for the dihedral angle at the peptide bond which can be used in NAMD. In the following, we will describe how t ...
Sequence Similarity Searching: Understanding and Using Web
... • Sequences are split into words (default n=3) – Speed, computational efficiency ...
... • Sequences are split into words (default n=3) – Speed, computational efficiency ...
The Primary Structure of the Calcium Ion
... The isolation and characterization of the soluble peptides from the CNBr digest of the calcium ion-transporting adenosine triphosphatase protein of rabbit skeletal sarcoplasmic reticulum are described. The 562 unique residues of the protein were placed in sequences. The remaining part of the protein ...
... The isolation and characterization of the soluble peptides from the CNBr digest of the calcium ion-transporting adenosine triphosphatase protein of rabbit skeletal sarcoplasmic reticulum are described. The 562 unique residues of the protein were placed in sequences. The remaining part of the protein ...
World Index of BioMolecular Visualization Resources
... variability; homology modelling; immunoglobulin; domains; color-coded multiple sequence alignment. This site contains extensive tutorials and lectures on antibody structure coupled with analyses of sequence variability in antibodies. The site also has a very nice set of Microsoft EXCEL spreadsheets ...
... variability; homology modelling; immunoglobulin; domains; color-coded multiple sequence alignment. This site contains extensive tutorials and lectures on antibody structure coupled with analyses of sequence variability in antibodies. The site also has a very nice set of Microsoft EXCEL spreadsheets ...
Field Guide to Protein Folds
... The calponin homology (CH) domain has an all α-helical architecture dominated by 4 α helices each comprising 11–18 residues connected by relatively long loops. A further three shorter and less well ordered α helices are also present. Often found in pairs they form the F-actin-binding region of prote ...
... The calponin homology (CH) domain has an all α-helical architecture dominated by 4 α helices each comprising 11–18 residues connected by relatively long loops. A further three shorter and less well ordered α helices are also present. Often found in pairs they form the F-actin-binding region of prote ...
DLocalMotif: a discriminative approach for discovering local motifs in
... Technically, represents tolerance to local motif shifts. In the extreme, if no shift is accepted ( ¼ 0), a sequence profile of the alignment would suffice to identify the motif. At the other extreme, the motif can shift arbitrarily over the sequence ( ¼ L k þ 1), meaning that no guidance is pr ...
... Technically, represents tolerance to local motif shifts. In the extreme, if no shift is accepted ( ¼ 0), a sequence profile of the alignment would suffice to identify the motif. At the other extreme, the motif can shift arbitrarily over the sequence ( ¼ L k þ 1), meaning that no guidance is pr ...
The Structure of Human Prions: From Biology to Structural Models
... 121–231) by NMR spectroscopy. For all species analyzed, the structure of recPrP consists of three α-helices (amino acids 144–154, 175–193 and 200–219) and a small antiparallel β-sheet (amino acids 128–131 and 161–164) [78]. It has an amino-terminal signal peptide (amino acids 1–23), a more or less f ...
... 121–231) by NMR spectroscopy. For all species analyzed, the structure of recPrP consists of three α-helices (amino acids 144–154, 175–193 and 200–219) and a small antiparallel β-sheet (amino acids 128–131 and 161–164) [78]. It has an amino-terminal signal peptide (amino acids 1–23), a more or less f ...
Shelef, Katie: A Critical Analysis of Degenerate Primer Design Programs
... degeneracy and coverage (the number of input sequences that can be amplified by the primer). From one perspective, the goal of degenerate primer design is to match and amplify as many of the input sequences as possible. Primers of high degeneracy are favored because this allows a greater number of i ...
... degeneracy and coverage (the number of input sequences that can be amplified by the primer). From one perspective, the goal of degenerate primer design is to match and amplify as many of the input sequences as possible. Primers of high degeneracy are favored because this allows a greater number of i ...
Evolution of the Aldose Reductase-Related Gecko Eye Lens Protein
... identification of 65 significantly related proteins. An initial alignment and phylogenetic tree constructed from these sequences (not shown) confirmed that this superfamily of proteins, the aldo-keto reductases, is highly divergent, with multiple representatives in diverse proand eukaryotes. However ...
... identification of 65 significantly related proteins. An initial alignment and phylogenetic tree constructed from these sequences (not shown) confirmed that this superfamily of proteins, the aldo-keto reductases, is highly divergent, with multiple representatives in diverse proand eukaryotes. However ...
Structure-Based Prediction of Asparagine and Aspartate
... However, modeling of long CDR loops is prone to large modeling uncertainties, possibly due to the high inherent flexibility of such loops [81–84]. Therefore, all CDRs were subjected to an additional loop modeling procedure [85] (Materials and Methods), yielding a five-membered homology model ensembl ...
... However, modeling of long CDR loops is prone to large modeling uncertainties, possibly due to the high inherent flexibility of such loops [81–84]. Therefore, all CDRs were subjected to an additional loop modeling procedure [85] (Materials and Methods), yielding a five-membered homology model ensembl ...
Biological significance of structural differences between two highly
... in called Uev1D30, would provide insight into whether these subtle differences might come together in three dimensions to constitute a sufficiently distinct surface. The structure of Uev1D30 was solved by molecular replacement using a poly-alanine model of Mms2 (PDB accession number: 1J74). The densi ...
... in called Uev1D30, would provide insight into whether these subtle differences might come together in three dimensions to constitute a sufficiently distinct surface. The structure of Uev1D30 was solved by molecular replacement using a poly-alanine model of Mms2 (PDB accession number: 1J74). The densi ...
PDF
... by BLAST is expected to contain such homolog-specific and position-specific information. An MSA can be transformed into a position-specific scoring matrix (PSSM), which is a more sophisticated model for sequence similarity search than the substitution matrix because scores for amino-acids are modele ...
... by BLAST is expected to contain such homolog-specific and position-specific information. An MSA can be transformed into a position-specific scoring matrix (PSSM), which is a more sophisticated model for sequence similarity search than the substitution matrix because scores for amino-acids are modele ...
Chapter 1: Biological Introduction: RING domain proteins
... the ubiquitination of the substrate. At least three different classes of E3 ligases have been found that mediate substrate ubiquitination. These E3 enzymes differ in the domain that recognizes the E2 enzymes, which can be a RING, a PHD (plant homeodomain) or a HECT (Homologous to E6AP COOH terminus) ...
... the ubiquitination of the substrate. At least three different classes of E3 ligases have been found that mediate substrate ubiquitination. These E3 enzymes differ in the domain that recognizes the E2 enzymes, which can be a RING, a PHD (plant homeodomain) or a HECT (Homologous to E6AP COOH terminus) ...
Characterization of Proteins Structurally Related to Human N
... fraction was confirmed by Cellogel electrophoresis as described by Braidman et al. (1974). The recovery of protein was 75-77% of that applied (range from three experiments). Under these conditions the serologically unrelated hexosaminidase C is not recovered from the DEAE-cellulose column (Braidman ...
... fraction was confirmed by Cellogel electrophoresis as described by Braidman et al. (1974). The recovery of protein was 75-77% of that applied (range from three experiments). Under these conditions the serologically unrelated hexosaminidase C is not recovered from the DEAE-cellulose column (Braidman ...
High pKa variability of cysteine residues in structural databases and
... these oxidations are effectively counteracted through natural defensive mechanisms [9]; however, intense and/or persistent levels of ROS stress ultimately lead to protein damage (misfolding, cross-linkages, inactivation of functional residues) [10,11]. A critically important aspect of Cys reactivity ...
... these oxidations are effectively counteracted through natural defensive mechanisms [9]; however, intense and/or persistent levels of ROS stress ultimately lead to protein damage (misfolding, cross-linkages, inactivation of functional residues) [10,11]. A critically important aspect of Cys reactivity ...
Molecular insights into RNA and DNA helicase evolution from the
... of helicases belonging to different SF1 and SF2 families (Fairman-Williams et al., 2010). Two other SF1 (Pif1-like and Upf1-like) and four other SF2 (Ski2-like; RecG-like; T1R; and Rad3/XPD) families have been identified (Fairman-Williams et al., 2010). Helicase core domains 1 and 2 are colored ligh ...
... of helicases belonging to different SF1 and SF2 families (Fairman-Williams et al., 2010). Two other SF1 (Pif1-like and Upf1-like) and four other SF2 (Ski2-like; RecG-like; T1R; and Rad3/XPD) families have been identified (Fairman-Williams et al., 2010). Helicase core domains 1 and 2 are colored ligh ...
InterPro Presentation - European Bioinformatics Institute
... Short sequences typically repeated within a protein ...
... Short sequences typically repeated within a protein ...
Retention of the Cis Proline Conformation in Tripeptide Fragments of
... Clearly, the ability to constrain a peptide group to a single unique confirmation is of considerable utility. A number of attempts have been made to constrain the X-Pro peptide group to a single conformation.23-31 Proline analogues such as methanoproline24,25 and oxazolidine-4-carboxylic acid31 are ...
... Clearly, the ability to constrain a peptide group to a single unique confirmation is of considerable utility. A number of attempts have been made to constrain the X-Pro peptide group to a single conformation.23-31 Proline analogues such as methanoproline24,25 and oxazolidine-4-carboxylic acid31 are ...
View PDF - DNA and Natural Algorithms Group
... different ATP binding proteins share the Rossman fold. Indeed, a closer structural examination reveals many similarities between the ways in which RNA molecules bind adenosine and proteins bind adenosine (Marshall et al., 1997). In each case, hydrogen bonding and stacking are the two dominant factor ...
... different ATP binding proteins share the Rossman fold. Indeed, a closer structural examination reveals many similarities between the ways in which RNA molecules bind adenosine and proteins bind adenosine (Marshall et al., 1997). In each case, hydrogen bonding and stacking are the two dominant factor ...
The UUAG-specific RNA Binding Protein, Heterogeneous Nuclear
... common groups of RNA binding proteins is the RBD class proteins (2). They possess a CS-RBD (consensus sequence-RNA binding domain) motif, which is typically 80 –90 amino acids. Two short sequences, RNP 2 octamer and RNP 1 hexamer, have been found to be conserved among different RBDs. Several RBDs ar ...
... common groups of RNA binding proteins is the RBD class proteins (2). They possess a CS-RBD (consensus sequence-RNA binding domain) motif, which is typically 80 –90 amino acids. Two short sequences, RNP 2 octamer and RNP 1 hexamer, have been found to be conserved among different RBDs. Several RBDs ar ...
Statistical Analysis of Amino Acid Patterns in Transmembrane
... expectancies of all pairs and triplets of residues in individual sequences, taking into account differential sequence composition and the substantial effect of ®nite length in short segments. We found that the number of signi®cantly over and under-represented pairs and triplets was much greater than ...
... expectancies of all pairs and triplets of residues in individual sequences, taking into account differential sequence composition and the substantial effect of ®nite length in short segments. We found that the number of signi®cantly over and under-represented pairs and triplets was much greater than ...
Print
... The -helix has intra-chain hydrogen bonds between the ‘H’ of NH and ‘O’ of CO in every 4th residue. In sheets, the backbone is made to zigzag such that chains are arranged side by side for hydrogen bonding. ...
... The -helix has intra-chain hydrogen bonds between the ‘H’ of NH and ‘O’ of CO in every 4th residue. In sheets, the backbone is made to zigzag such that chains are arranged side by side for hydrogen bonding. ...
The PRT protein family Sangita C Sinha* and Janet L Smith
... Sangita C Sinha* and Janet L Smith† Members of the homologous PRT family are catalytic and regulatory proteins involved in nucleotide synthesis and salvage. New crystal structures have revealed key elements of PRT protein function, as well as glimpses of how the fold has evolved to perform both cata ...
... Sangita C Sinha* and Janet L Smith† Members of the homologous PRT family are catalytic and regulatory proteins involved in nucleotide synthesis and salvage. New crystal structures have revealed key elements of PRT protein function, as well as glimpses of how the fold has evolved to perform both cata ...
Protein structure is conceptually divided into four
... A simple illustration of the way eight b strands are arranged in a jelly roll motif. (a) The eight b strands are drawn as arrows along two edges of a strip of paper. The strands are arranged such that strand 1 is opposite strand 8, etc. The b strands are separated by loop regions. (b) The strip of p ...
... A simple illustration of the way eight b strands are arranged in a jelly roll motif. (a) The eight b strands are drawn as arrows along two edges of a strip of paper. The strands are arranged such that strand 1 is opposite strand 8, etc. The b strands are separated by loop regions. (b) The strip of p ...
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.