Description of the KDD-Cup 2004 Protein Data
... Description of the KDD-Cup 2004 Protein Data Author: Ron Elber, Department of Computer Science, Cornell University The data are generated by the program LOOPP (Learning Observing and Outputting Protein Patterns) that is a product of the group of Ron Elber, Computer Science, Cornell University. The L ...
... Description of the KDD-Cup 2004 Protein Data Author: Ron Elber, Department of Computer Science, Cornell University The data are generated by the program LOOPP (Learning Observing and Outputting Protein Patterns) that is a product of the group of Ron Elber, Computer Science, Cornell University. The L ...
第五屆生物物理新知研討會
... Department of Biological Science & Technology,Institute of Bioinformatics, National Chiao Tung University, HsinChu, Taiwan ...
... Department of Biological Science & Technology,Institute of Bioinformatics, National Chiao Tung University, HsinChu, Taiwan ...
Combinatorial docking approach for structure prediction of large
... I became interested in this paper because of the simplicity of the algorithm, called CombDock (for Combinatorial Docking). For a large protein it uses a dissection algorithm to break it down into smaller pieces. The structure of these pieces is then determined computationally. This step is nice beca ...
... I became interested in this paper because of the simplicity of the algorithm, called CombDock (for Combinatorial Docking). For a large protein it uses a dissection algorithm to break it down into smaller pieces. The structure of these pieces is then determined computationally. This step is nice beca ...
Hands-on Exercise: Locating Protein Information
... A variant of this protein with mutations in its amino acid sequence has been isolated (see link http://www.hsls.pitt.edu/guides/genetics/tutorials). ...
... A variant of this protein with mutations in its amino acid sequence has been isolated (see link http://www.hsls.pitt.edu/guides/genetics/tutorials). ...
Exercises in MBV-INF 4410/9410/9410A
... (MUTYH) (546 aa), N-glycosylase/DNA lyase isoform 1a (OGG1) (345 aa) and methylCpG-binding domain protein 4 (MBD4) (580 aa). The MBD4 protein may have an E-value worse than the PSI-BLAST threshold, but is still a homolog. Give the sequences short names. b) Make a multiple sequence alignment of the f ...
... (MUTYH) (546 aa), N-glycosylase/DNA lyase isoform 1a (OGG1) (345 aa) and methylCpG-binding domain protein 4 (MBD4) (580 aa). The MBD4 protein may have an E-value worse than the PSI-BLAST threshold, but is still a homolog. Give the sequences short names. b) Make a multiple sequence alignment of the f ...
341- INTRODUCTION TO BIOINFORMATICS Overview of the …
... – Scale-free Networks (SF) – Hierarchical Networks – Geometric Networks (GEO) – Generalized Random Networks (ERDD) – Geometric Networks with Gene Duplication / Divergence Events(GEOGD) – Scale-free Networks with Gene Duplications/Divergence Events (SFGD) – Stickiness-index based Networks (STICKY) ...
... – Scale-free Networks (SF) – Hierarchical Networks – Geometric Networks (GEO) – Generalized Random Networks (ERDD) – Geometric Networks with Gene Duplication / Divergence Events(GEOGD) – Scale-free Networks with Gene Duplications/Divergence Events (SFGD) – Stickiness-index based Networks (STICKY) ...
Knuffke Prezi- Macromolecules
... Organic Compounds Substances which contain Carbon. All living things contain Carbon, it is known as the backbone of life. ...
... Organic Compounds Substances which contain Carbon. All living things contain Carbon, it is known as the backbone of life. ...
Estimation of the protein secondary structure in aqueous solutions
... The secondary structure of proteins is very important for their proper functioning. The investigation of the secondary structure gives us an insight into the mechanisms of protein functioning in the living cell. IR absorption spectroscopy provides the opportunity to identify a large number of types ...
... The secondary structure of proteins is very important for their proper functioning. The investigation of the secondary structure gives us an insight into the mechanisms of protein functioning in the living cell. IR absorption spectroscopy provides the opportunity to identify a large number of types ...
Optimizing Genetic Algorithm Parameters for Multiple
... more protein or nucleic acid sequences that maximizes the similarities between them. MSAs are used in protein structure modeling, functional prediction and phylogenetic analysis, such as in the studies of [2, 4], which enables us to determine the evolutionary relationships between the sequences bein ...
... more protein or nucleic acid sequences that maximizes the similarities between them. MSAs are used in protein structure modeling, functional prediction and phylogenetic analysis, such as in the studies of [2, 4], which enables us to determine the evolutionary relationships between the sequences bein ...
Lecture 1: Fundamentals of Protein Structure
... Not conserved (can be many different residues in different species) ...
... Not conserved (can be many different residues in different species) ...
Key Points Folding
... Key Points Prions and Protein Folding • Protein structure (primary, secondary, tertiary) • Proteins have many possible conformations (ways to fold up into a 3D structure) • Proteins can spontaneously fold into the correct (biologically functional) 3D structure demonstrated by Christian Anfinsen in t ...
... Key Points Prions and Protein Folding • Protein structure (primary, secondary, tertiary) • Proteins have many possible conformations (ways to fold up into a 3D structure) • Proteins can spontaneously fold into the correct (biologically functional) 3D structure demonstrated by Christian Anfinsen in t ...
Using Computers to teach Undergraduates about Biological Molecules
... approaches. Students can normally determine the sequence of a polypeptide of 70-80 residues in about two hours. Reasonably realistic yields and 'carry over' contaminations make this an attractive program despite its age. The utility of prediction methods in teaching protein In addition, the structur ...
... approaches. Students can normally determine the sequence of a polypeptide of 70-80 residues in about two hours. Reasonably realistic yields and 'carry over' contaminations make this an attractive program despite its age. The utility of prediction methods in teaching protein In addition, the structur ...
Ch. 3 Study Guide
... 6. How is the structure of a phospholipid molecule different from that of a triglyceride molecule? ...
... 6. How is the structure of a phospholipid molecule different from that of a triglyceride molecule? ...
class04
... later divergence high sequence similarity E.g., M[250] is known not to reflect well long period changes (see p. 43 at Durbin et al). Does ...
... later divergence high sequence similarity E.g., M[250] is known not to reflect well long period changes (see p. 43 at Durbin et al). Does ...
How to classify proteins on basis of structure?
... How to recognize 3D motifs and patterns? How to use bioinformatics databases to help in 3D structure determination? • How to predict which proteins will express well or produce stable, folded molecules? ...
... How to recognize 3D motifs and patterns? How to use bioinformatics databases to help in 3D structure determination? • How to predict which proteins will express well or produce stable, folded molecules? ...
Lecture_11
... • FtsZ and Tubulin have limited sequence similarity and would not be identified as homologous proteins by sequence analysis. ...
... • FtsZ and Tubulin have limited sequence similarity and would not be identified as homologous proteins by sequence analysis. ...
w0506_tutorial8
... Can BLAST help us to predict its SS? 2. Use any secondary structure prediction method to predict the secondary structure of 1O8V and compare it to the solved structure. NOTICE! The secondary structure definition in PDB is given in a 7 letter code instead of 3 letter code (H, E, C). For comparison pu ...
... Can BLAST help us to predict its SS? 2. Use any secondary structure prediction method to predict the secondary structure of 1O8V and compare it to the solved structure. NOTICE! The secondary structure definition in PDB is given in a 7 letter code instead of 3 letter code (H, E, C). For comparison pu ...
Workshop#4
... Note: it is possible that two proteins share a high degree of similarity but have two different functions. For example, human gamma-crystallin is a lens protein that has no known enzymatic activity. It shares a high percentage of identity with E. coli quinone oxidoreductase. These proteins likely ha ...
... Note: it is possible that two proteins share a high degree of similarity but have two different functions. For example, human gamma-crystallin is a lens protein that has no known enzymatic activity. It shares a high percentage of identity with E. coli quinone oxidoreductase. These proteins likely ha ...
The World of Chemistry
... Episode 24 - The Genetic Code https://www.learner.org/vod/vod_window.html?pid=816 1. What are some of the ways mentioned that proteins are used in our bodies? ...
... Episode 24 - The Genetic Code https://www.learner.org/vod/vod_window.html?pid=816 1. What are some of the ways mentioned that proteins are used in our bodies? ...
A Novel Scoring Function for Predicting the Conformation of Pairs of
... proteins are tightly packed. We present a scoring function and a computational methodology for predicting the tertiary fold of a pair of α-helices, such that its chances of being tightly packed are maximized. Since the number of TM protein structures solved to date is small, it seems unlikely that a ...
... proteins are tightly packed. We present a scoring function and a computational methodology for predicting the tertiary fold of a pair of α-helices, such that its chances of being tightly packed are maximized. Since the number of TM protein structures solved to date is small, it seems unlikely that a ...
Identification of Domains using Structural Data
... • Full lines indicate protein backbone. • Neighboring residues within radius r are connected by dashed lines. • Connections between i and i + 2 have been omitted for clarity. • Label evolution is done without inverse distance weighting. ...
... • Full lines indicate protein backbone. • Neighboring residues within radius r are connected by dashed lines. • Connections between i and i + 2 have been omitted for clarity. • Label evolution is done without inverse distance weighting. ...
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.