Exam questions used in the past
... This page contains a randomly selected series of exam questions that we have used in the past in real exams, and that you should be able to answer by now. Exam questions used in the past: 1. A colleague has sequenced a novel gene. He comes to you and asks for help. What do you do first and why? ...
... This page contains a randomly selected series of exam questions that we have used in the past in real exams, and that you should be able to answer by now. Exam questions used in the past: 1. A colleague has sequenced a novel gene. He comes to you and asks for help. What do you do first and why? ...
Sequencing genomes
... And the same is true for Dayhoff’s model of evolution. If we need to obtain probability matrices for higher percentage of accepted mutations (i.e. covering longer evolutionary time), we do matrix powers. Let’s say we want PAM120 – 120 mutations fixed on average per 100 residues. We do PAM1120. ...
... And the same is true for Dayhoff’s model of evolution. If we need to obtain probability matrices for higher percentage of accepted mutations (i.e. covering longer evolutionary time), we do matrix powers. Let’s say we want PAM120 – 120 mutations fixed on average per 100 residues. We do PAM1120. ...
Supplementary Table 1: A complete list of proteins identified with
... MOLM-13 cells treated with DMSO (control) were labeled with light isotopes of amino acids (L), and nutlin-treated cells were labeled with heavy isotopes of amino acids (H); the reported regulation of proteins in response to nutlin-3 is the normalized H/L ratio, given as fold induction of control. Pr ...
... MOLM-13 cells treated with DMSO (control) were labeled with light isotopes of amino acids (L), and nutlin-treated cells were labeled with heavy isotopes of amino acids (H); the reported regulation of proteins in response to nutlin-3 is the normalized H/L ratio, given as fold induction of control. Pr ...
G Protein Coupled Receptors
... Simple Methods for Predicting the Secondary Structure of Globular Proteins J. Garnier, D.J. Osguthorpe and B Robson Journal of Molecular Biology (1978); 120, 97-120 ...
... Simple Methods for Predicting the Secondary Structure of Globular Proteins J. Garnier, D.J. Osguthorpe and B Robson Journal of Molecular Biology (1978); 120, 97-120 ...
Protein Aggregation in High-Protein Caramel
... Here, the caramel takes on a tapioca-like structure, with large visible aggregates of protein structures (Figure 1), as it loses its desirable smooth texture. There are two general categories of proteins in milk — the caseins (≈80%) and the serum proteins (≈20%). The various casein proteins form int ...
... Here, the caramel takes on a tapioca-like structure, with large visible aggregates of protein structures (Figure 1), as it loses its desirable smooth texture. There are two general categories of proteins in milk — the caseins (≈80%) and the serum proteins (≈20%). The various casein proteins form int ...
Slides
... If the target and the template share more than 50% of their sequences, predictions usually are of high quality and have been shown to be as accurate as low-resolution Xray predictions. For 30–50% sequence identity more than 80% of the C-atoms can be expected to be within 3.5 ˚A of their true positio ...
... If the target and the template share more than 50% of their sequences, predictions usually are of high quality and have been shown to be as accurate as low-resolution Xray predictions. For 30–50% sequence identity more than 80% of the C-atoms can be expected to be within 3.5 ˚A of their true positio ...
E value - Webcourse
... Use a heuristic (approximate) algorithm to discard most irrelevant sequences and perform the exact algorithm on the small group of remaining sequences. ...
... Use a heuristic (approximate) algorithm to discard most irrelevant sequences and perform the exact algorithm on the small group of remaining sequences. ...
Word Doc - Biochemistry
... residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several hundred residues in multi-functional proteins. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filam ...
... residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several hundred residues in multi-functional proteins. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filam ...
R032 Publication Only Basic Science: Biofilm Key proteins of
... equipment AB SCIEX MALDI TOF/TOF 5800 System (Applied Biosystems). The spectra obtained were processed using the Protein Pilot and the sequences were found in the Swiss databank. Results: The proteomic analysis revealed that the samples exhibited different protein profiles, with an increased protein ...
... equipment AB SCIEX MALDI TOF/TOF 5800 System (Applied Biosystems). The spectra obtained were processed using the Protein Pilot and the sequences were found in the Swiss databank. Results: The proteomic analysis revealed that the samples exhibited different protein profiles, with an increased protein ...
Western blot analysis
... 10-4 was used to define hits in a given round of iterations to be included in a position-specific scoring matrix that was used as query in the next iteration. The resulting homologues of the query were defined using an E value cut-off of 10-4. Remote structural homology between Etk, Wzc, MinD, ParA ...
... 10-4 was used to define hits in a given round of iterations to be included in a position-specific scoring matrix that was used as query in the next iteration. The resulting homologues of the query were defined using an E value cut-off of 10-4. Remote structural homology between Etk, Wzc, MinD, ParA ...
Three Dimensional Protein Structures
... Ehlers-Danlos syndromes, hyperextensible joints and skin, Indian rubberman Osteoarthritis - cartilage. ...
... Ehlers-Danlos syndromes, hyperextensible joints and skin, Indian rubberman Osteoarthritis - cartilage. ...
LOYOLA COLLEGE (AUTONOMOUS), CHENNAI – 600 034
... 12. Explain Blast and types of blasts. 13. Give a detail account of FASTA. 14. Write notes on DNA sequence databases. 15. Describe Multiple Sequence Alignment and its significance. 16. Give an account on information resources. PART-C Answer any TWO of the following ...
... 12. Explain Blast and types of blasts. 13. Give a detail account of FASTA. 14. Write notes on DNA sequence databases. 15. Describe Multiple Sequence Alignment and its significance. 16. Give an account on information resources. PART-C Answer any TWO of the following ...
Finding an upper bound for the number of contacts in hydrophobic
... It is believed that the functional properties of the protein are dependent on its structure. Therefore, it is critical to predict the protein's structure to understand the functional properties. One of the most widely studied protein structure prediction models is the hydrophobic-hydrophilic (HP) mo ...
... It is believed that the functional properties of the protein are dependent on its structure. Therefore, it is critical to predict the protein's structure to understand the functional properties. One of the most widely studied protein structure prediction models is the hydrophobic-hydrophilic (HP) mo ...
Two Rules on Protein-Ligand Interactions Xiaodong Pang1, 2
... Understanding the ruling principles of interaction between a target protein and a ligand is of paramount importance in drug discovery efforts. So far, in finding a real ligand for a given target protein, we are limited to experimental screening from a large number of small molecules, or through free ...
... Understanding the ruling principles of interaction between a target protein and a ligand is of paramount importance in drug discovery efforts. So far, in finding a real ligand for a given target protein, we are limited to experimental screening from a large number of small molecules, or through free ...
Protein folding
... 3-D structure of a protein is determined by its amino acid sequence (primary structure). The function of a protein depends on its structure. A protein exists in one or a few stable structural forms (conformations). A protein’s conformation is stabilized largely by weak interactions. Protei ...
... 3-D structure of a protein is determined by its amino acid sequence (primary structure). The function of a protein depends on its structure. A protein exists in one or a few stable structural forms (conformations). A protein’s conformation is stabilized largely by weak interactions. Protei ...
Clustering of Proteins
... Numerous genome-sequencing projects have led to a huge growth in the size of protein databases. Manual annotation of the sequences found in these databases is expensive and not very feasible. Thus, there is a need for developing reliable algorithms that automate the functional classification of thes ...
... Numerous genome-sequencing projects have led to a huge growth in the size of protein databases. Manual annotation of the sequences found in these databases is expensive and not very feasible. Thus, there is a need for developing reliable algorithms that automate the functional classification of thes ...
The_Structure_of_Protein_Activity
... a) The solubility of many proteins in water. b) The precise 3D structure of those enzymes which are proteins. c) The eleasticity of natural fibres such as wool and silk? ...
... a) The solubility of many proteins in water. b) The precise 3D structure of those enzymes which are proteins. c) The eleasticity of natural fibres such as wool and silk? ...
Growth Hormone Releasing Hormone (GHRH) - Cloud
... Endotoxin Level: <1.0EU per 1μg (determined by the LAL method). Formulation: Supplied as lyophilized form in PBS, pH7.4, containing 5% sucrose, 0.01% sarcosyl. Predicted isoelectric point point:: 8.7 Predicted Molecular Mass: 37.4kDa Accurate Molecular Mass: 43.5kDa as determined by SDS-PAGE reducin ...
... Endotoxin Level: <1.0EU per 1μg (determined by the LAL method). Formulation: Supplied as lyophilized form in PBS, pH7.4, containing 5% sucrose, 0.01% sarcosyl. Predicted isoelectric point point:: 8.7 Predicted Molecular Mass: 37.4kDa Accurate Molecular Mass: 43.5kDa as determined by SDS-PAGE reducin ...
Protein Origami
... replicate the HIV virus. Cancer is linked to damage in proteins that inhibit uncontrolled cell growth. Alzheimer’s disease is believed to be related to malfunctioning proteins that are normally part of healthy brain cells. The duties proteins perform or do not perform are governed by the shapes into ...
... replicate the HIV virus. Cancer is linked to damage in proteins that inhibit uncontrolled cell growth. Alzheimer’s disease is believed to be related to malfunctioning proteins that are normally part of healthy brain cells. The duties proteins perform or do not perform are governed by the shapes into ...
Multiple Choice Questions
... The effective magnetic field of each nuclei varies due to local shielding effects, i.e. the unique chemical (or magnetic) environment of each proton. ...
... The effective magnetic field of each nuclei varies due to local shielding effects, i.e. the unique chemical (or magnetic) environment of each proton. ...
Carbs, Lipids, and Proteins
... are also composed of C, H, & O but the ratio is less predictable than in carbs Primary use = as a fuel for production of ATP and for fuel storage. Secondary use = as structural components for building cell membranes and hormones Examples: The most common type of lipid we consume as food and ...
... are also composed of C, H, & O but the ratio is less predictable than in carbs Primary use = as a fuel for production of ATP and for fuel storage. Secondary use = as structural components for building cell membranes and hormones Examples: The most common type of lipid we consume as food and ...
Presentation - Harlem Children Society
... Protein analysis of HIF1 The predicted structure on the previous page displays the HIF1 protein, which is the main regulator of hypoxia-induced gene expression as well as the DNA binding protein. It is a heterodimeric transcription factor composed of HIF1A. The HIF1 protein expressed by the struc ...
... Protein analysis of HIF1 The predicted structure on the previous page displays the HIF1 protein, which is the main regulator of hypoxia-induced gene expression as well as the DNA binding protein. It is a heterodimeric transcription factor composed of HIF1A. The HIF1 protein expressed by the struc ...
Modelling Proteomes
... expanded irregular unique shape precisely ordered stable/functional globular/compact helices and sheets ...
... expanded irregular unique shape precisely ordered stable/functional globular/compact helices and sheets ...
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.