Finding Regulatory Sites - TAMU Computer Science Faculty Pages
... Although the structure of the HMM is pre-determined, it is necessary to provide estimates of other parameters (such as transition probabilities) via a set of training examples. ...
... Although the structure of the HMM is pre-determined, it is necessary to provide estimates of other parameters (such as transition probabilities) via a set of training examples. ...
Lecture 9 Database Searching Database Searching for Similar
... significant ones • An efficient search tree is made using the high scoring words • The database is searched to find matches for the 50 significant words. These are used as seeds for ungapped alignment with the query sequence ...
... significant ones • An efficient search tree is made using the high scoring words • The database is searched to find matches for the 50 significant words. These are used as seeds for ungapped alignment with the query sequence ...
Slide 1
... • Refinement – How well do atomic coordinates agree with data? – R-value • Should be 20% or less ...
... • Refinement – How well do atomic coordinates agree with data? – R-value • Should be 20% or less ...
Protein Structure Prediction (10 points total)
... polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA ...
... polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA ...
PPT - FLI - Leibniz Institute for Age Research
... Comprehensive bending classification of nucleic acid double helix structures Versatile search options allowing the direct search for identifiers/names from PDB, NDB, UniProt, Pfam, SMART, SCOP, GO ...
... Comprehensive bending classification of nucleic acid double helix structures Versatile search options allowing the direct search for identifiers/names from PDB, NDB, UniProt, Pfam, SMART, SCOP, GO ...
PSIpred Input
... Align all sequences to the query sequence as the template. Assign weights to the sequences Construct position specific scoring matrix ...
... Align all sequences to the query sequence as the template. Assign weights to the sequences Construct position specific scoring matrix ...
Sequence Alignment Techniques
... • Each iteration discovers intermediate sequences that are used in a sequence profile to discover more distant relatives of the query sequence in subsequent iterations • Potential problems with PSI-BLAST are associated with the potential for unrelated sequences to pollute the iterative search, and d ...
... • Each iteration discovers intermediate sequences that are used in a sequence profile to discover more distant relatives of the query sequence in subsequent iterations • Potential problems with PSI-BLAST are associated with the potential for unrelated sequences to pollute the iterative search, and d ...
PowerPoint 0.3MB - The Biomolecular Modeling & Computational
... • Prediction of secondary structure – relation of protein sequence to structure – statistically based prediction – pattern based prediction ...
... • Prediction of secondary structure – relation of protein sequence to structure – statistically based prediction – pattern based prediction ...
Principles of Protein Structure
... Middle Domain of eIF4G - scaffold protein for translation initiation factors. ...
... Middle Domain of eIF4G - scaffold protein for translation initiation factors. ...
No Slide Title
... – High-scoring database sequences are assumed to be evolutionary related to the query sequence. – If sequences are related by divergence from a common ancestor, there are said to be homologous. ...
... – High-scoring database sequences are assumed to be evolutionary related to the query sequence. – If sequences are related by divergence from a common ancestor, there are said to be homologous. ...
secstruct
... Why: experimental methods, X-ray crystallography or NMR spectroscopy, are very time-consuming and relatively expensive. ...
... Why: experimental methods, X-ray crystallography or NMR spectroscopy, are very time-consuming and relatively expensive. ...
Align sequence to structure - Computational Bioscience Program
... • Threading: Align sequence to structure (templates) For each alignment, the probability that that each amino acid residue would occur in such an environment is calculated based on observed preferences in determined structures. § Rationale: • Limited number of basic folds found in nature • Amino aci ...
... • Threading: Align sequence to structure (templates) For each alignment, the probability that that each amino acid residue would occur in such an environment is calculated based on observed preferences in determined structures. § Rationale: • Limited number of basic folds found in nature • Amino aci ...
Protein Structure
... Three separate programs, DSSP, STRIDE, and DEFINE, all use different definitions, and thus come up with somewhat different results, mostly at the ends of the structures. Hydrogen-bonding patterns, dihedral angles (the and angles of the alpha carbons in the backbone), and interatomic distances co ...
... Three separate programs, DSSP, STRIDE, and DEFINE, all use different definitions, and thus come up with somewhat different results, mostly at the ends of the structures. Hydrogen-bonding patterns, dihedral angles (the and angles of the alpha carbons in the backbone), and interatomic distances co ...
Slide
... • Protein Folding is the process by which a sequence of amino acids conforms to a three-dimensional shape. • Anfinsen’s hypothesis suggests that proteins fold to a minimum energy state. • So, our goal is to find a conformation with minimum energy. • We want to investigate algorithmic aspects of simu ...
... • Protein Folding is the process by which a sequence of amino acids conforms to a three-dimensional shape. • Anfinsen’s hypothesis suggests that proteins fold to a minimum energy state. • So, our goal is to find a conformation with minimum energy. • We want to investigate algorithmic aspects of simu ...
File
... polypeptides, which makes up proteins. • Each type of a.a. differs in the composition of the variable side chain (R). • Different side chains will have distinct chemical properties (charged, nonpolar). • The protein will fold and function differently according to its specific position within the pol ...
... polypeptides, which makes up proteins. • Each type of a.a. differs in the composition of the variable side chain (R). • Different side chains will have distinct chemical properties (charged, nonpolar). • The protein will fold and function differently according to its specific position within the pol ...
Sequence database similarity search
... FIG. 1. Identification of sequence similarities by FASTA. The four steps used by the FASTA program to calculate the initial and optimal similarity scores between two sequences are shown. (A) Identify regions of identity. (B) Scan the regions using a scoring ...
... FIG. 1. Identification of sequence similarities by FASTA. The four steps used by the FASTA program to calculate the initial and optimal similarity scores between two sequences are shown. (A) Identify regions of identity. (B) Scan the regions using a scoring ...
lecture03_14
... – Searching an mRNA against HG requires ~1012 cells -Even efficient exact algorithms will be extremely slow when preformed millions of times even with parallel computing. ...
... – Searching an mRNA against HG requires ~1012 cells -Even efficient exact algorithms will be extremely slow when preformed millions of times even with parallel computing. ...
Protein Threading Optimization Using
... refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Threading - The basis of template matching method is Threading or Fold Recognition. Threading works ...
... refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Threading - The basis of template matching method is Threading or Fold Recognition. Threading works ...
Tertiary Structure - Rogue Community College
... • A result of interactions between side (R) chains that are widely separated within the peptide chain Covalent disulfide bonds - between 2 cysteine AA Salt bridges - between AA w/ charged side chains (acid & base AA) Hydrogen bonds - between AA with polar R groups Hydrophobic attractions - between N ...
... • A result of interactions between side (R) chains that are widely separated within the peptide chain Covalent disulfide bonds - between 2 cysteine AA Salt bridges - between AA w/ charged side chains (acid & base AA) Hydrogen bonds - between AA with polar R groups Hydrophobic attractions - between N ...
eGOR Predicting the total potential Energy of a Protein`s native State
... Background and Motivation ...
... Background and Motivation ...
Sequences Alignment, part A
... 2. Indel is the alignment of a letter to the sign ’-’ (gap). Indel stands for insertion/deletion, meaning a base was inserted or deleted in one of the sequences in comparison to the other. Note that it is possible to insert gaps also at the beginning or at the end of the sequences. 3. M ismatch is j ...
... 2. Indel is the alignment of a letter to the sign ’-’ (gap). Indel stands for insertion/deletion, meaning a base was inserted or deleted in one of the sequences in comparison to the other. Note that it is possible to insert gaps also at the beginning or at the end of the sequences. 3. M ismatch is j ...
DNA properties.
... Database based on domain architecture, defined as the sequential order of conserved domains in proteins. ...
... Database based on domain architecture, defined as the sequential order of conserved domains in proteins. ...
Post doctoral position for protein crystallographer
... We are looking for a trained protein crystallographer. The main project is the identification of inhibitors for the A chain of the cytotoxin called ricin. The project is reasonably well advanced with several modest inhibitors now known from virtual screening and high throughput screening of diversit ...
... We are looking for a trained protein crystallographer. The main project is the identification of inhibitors for the A chain of the cytotoxin called ricin. The project is reasonably well advanced with several modest inhibitors now known from virtual screening and high throughput screening of diversit ...
View video content as a PDF
... The Final 3-Dimensional Shape of the Protein Once the secondary structures of a protein have been folded, the model must be given the correct overall shape. When doing this it is very useful to refer back to the online visualization environment. This display can be edited to match what the final phy ...
... The Final 3-Dimensional Shape of the Protein Once the secondary structures of a protein have been folded, the model must be given the correct overall shape. When doing this it is very useful to refer back to the online visualization environment. This display can be edited to match what the final phy ...
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.