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Dynamic method dispatch based upon predicates ... Enclose the method body under the if's body ... these predicates in the method header, code becomes a lot ...
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JPred compiler. Eclipse. 8. Background: JPred. class Spy { void escape(Vehicle v) ... class Spy { void escape(Vehicle v) void escape(Vehicle v) when v@Flyable ...
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... Enzyme Family Classification by Support Vector Machines, ... http://www.compbio.dundee.ac.uk/~www-jpred/ Prediction method: Jnet; two fully connected, ...
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Transmembrane Helix: TMHMM, TMAP. 2D Prediction (a-helix, b-sheet, Coiled-coils): PHD, JPred ... Transmembrane Helix (http://www.cbs.dtu.dk/services/TMHMM/) 29 ...
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Chrissy Oriol. Lydia Shih. Sudhakar Reddy. Proteins. And Secondary Structure. Project Goals ... CHRISSY ORIOL. JNET AND JPRED. Multiple Alignement. Neural ...
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Title: PowerPoint Presentation Author: Valued Sony Customer Last modified by: njit Created Date: 4/29/2002 1:34:55 AM Document presentation format
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Structure Modeling and Bioimage informatics Unit 26 BIOL221T: Advanced Bioinformatics for Biotechnology Irene Gabashvili, PhD Visualization Cn3D UCSF Chimera ...
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Protein Secondary Structures Assignment and prediction Secondary Structure Elements Use of secondary structure Classification of protein structures Definition of ...
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PSI-PRED secondary structure prediction based on PSIBLAST ... Strand(E), Helix(H) and Coil(C) AA: RLMPHIKRSAIPVNHGQCRWEDNVDERTNCMIQYVLIMRD ...
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... P., Brunak, S., Frasconi, P., Soda, G. & Pollastri, G. (1999). Exploiting the past and the future in protein secondary structure prediction. Bioinformatics, ...
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Title: Secondary Structure Prediction methods based on Sequence Alone: A review Author: Madhavi Ganapathiraju Last modified by: Madhavi Ganapathiraju
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WWW and X GUIs. Comprehensive. Widely available. Similar ... Several GUIs (java, WWW, X) Excellent GUI including interactive graphical output. Comprehensive ...
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Protein Structure Prediction Sequence database searching Domain assignment Multiple sequence alignment Comparative or homology modeling Secondary structure prediction
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Homology: Similarity in characteristics resulting from shared ancestry. ... LIBRA I. http://www.ddbj.nig.ac.jp/htmls/Email/libra/LIBRA_I.html. UCLA DOE ...
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Quality Aware Sensor Database (QUASAR) Project** Sharad Mehrotra Department of Information and Computer Science University of California, Irvine
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From http://www.imb-jena.de. Helices. phi(deg) psi(deg) H-bond pattern ... 6-8 Percentage points increase in prediction accuracy over standard neural networks ...
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Homology search of Defensins among different species. HT05 Fall Research Training ... produced in primate leukocytes by the ligation of two truncated alpha-defensins. ...
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Theory and Computation in Molecular Biological Physics ... Kolinski & Skolnick: Proteins 32, 475 (1998) Monte Carlo simulations: Attempt move ...
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Objective - identify and describe all the physico-chemical, ... SCOP. http://scop.mrc-lmb.cam.ac.uk/scop/ Lecture 2.5. 20. Expression Databases. Swiss 2D Page ...
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Protein Structure Prediction PHD: Network 1 Sequence Structure 13x20 values 3 values Pa(i) Pb(i) Pc(i) Network1 PHD: Network 2 Structure Structure 3 values Pa(i ...
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Orientation can be predicted using 'positive inside' rule ... periplasmic side (space between inner & outer membrane in gram-negative bacteria) ...
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Sequence Analysis (II) Yuh-Shan Jou ( ) jou@ibms.sinica.edu.tw Institute of Biomedical Sciences, Academia Sinica
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RMSD = 0.2 dream on. A Good Protein Structure.. X-ray ... Results posted on the web and updated weekly. http://cubic.bioc.columbia.edu/eva. Lecture 3.2 ...
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A Two-stage Classifier for Protein -turn Prediction using Support Vector Machines ... Predicting -turns -turns are a type of coil. Frequent. Important in ...
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Hacking the Genome - Designer Proteins, Elite Organisms, and You. Russell Hanson ... and the amount of effort spent on protein folding, i.e. 'more time to hack' ...
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... P P ' ' ' ' P F ' P ... nn pFasF fpa p F pdtFFtddTTFeffTt s d d e n n ...
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Title: Fisica Computazionale applicata alle Macromolecole Author: biocomp Last modified by: Piero Created Date: 5/25/2003 2:13:37 PM Document presentation format
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Molecular Weight. Amino Acid Frequency. Isoelectric Point. UV ... Molecular Weight & Proteomics. 2-D Gel QTOF Mass Spectrometry. Amino Acid Frequency ...
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C'est un homologue de LuxR (25% d 'identit selon l 'alignement donn par ALIGN) ... L 'alignement BabR-LuxR permet de d finir sur la topologie les r sidus importants dans la ...
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Sample Protein: MEPAPSAGAELQPPLFANASDAYPSACPSAGANASGPPGARSASSLALAIAITAL ... n' most similar reference segment vectors are retrieved ...
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From Markov Chains to Hidden Markov Models (HMM) ... Hidden Markov Model. for protein sequences. three types ... E.g. SCOP http://scop.mrc-lmb.cam.ac.uk/scop ...
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Title: PowerPoint Presentation Author: Xiaole Shirley Liu Last modified by: Jun Liu Created Date: 1/3/2005 7:27:35 PM Document presentation format
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Used to calculate hydrophobicity ... Hydrophobicity Profile. Moving segment approach. Correlation of this technique with 3D structure ...
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From http://www.imb-jena.de. Helices. phi(deg) psi(deg) H-bond pattern ... N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 ...
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Protein structure prediction: The holy grail of bioinformatics * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * No long range affects * * * IgG ...
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Title: Bioinform tica Author: Daniel Guariz Pinheiro Last modified by: Daniel Guariz Pinheiro Created Date: 2/27/2006 5:59:01 PM Document presentation format
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BCB 444/544 F07 ISU Dobbs #21 - Protein Secondary Structure Prediction ... SCOP = Structural Classification of Proteins ... http://scop.mrc-lmb.cam.ac.uk/scop ...
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Hydrophobicity/membrane insertion. Antigenicity. Surface Accessibility ... Hydrophobicity. Membrane association/topology. Programs. PHDhtm. TopPred. TMHMM ...
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Visualizing and Analyzing CryoEM Density Maps
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Annotation to identify and describe all the physico-chemical, ... Roche/Boeringer. http://www.expasy.org/cgi-bin/search-biochem-index. EcoCyc. www.ecocyc.org ...
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CM: Comparative (homology) modeling. CM/FR: not PSI-BLAST (but ... Ab initio modeling methods ... most abundant high scoring models. Use output from a set ...
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Grew from a simple observation that certain amino acids or ... DSSP - Database of Secondary Structures for Proteins (swift.embl-heidelberg.de/dssp) ...
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Title: Presentaci n de PowerPoint Last modified by: Preferred Customer Document presentation format: On-screen Show Other titles: Times New Roman Arial Arial Unicode ...
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rate of evolution of different parts of protein structures ... sometimes 1.0 Angstrom RMSD (RMSD is the root mean square deviation between ...
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Fisica Computazionale applicata alle Macromolecole Reti Neurali per la predizione proteica Pier Luigi Martelli Universit di Bologna gigi@biocomp.unibo.it
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3,100,000 bases in total. Paper to appear in December (Science) ... The Web (BRONCO) http://redpoll.pharmacy.ualberta.ca/~aleung. Gene Prediction. 5'site ...
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(Bio)-applications of high-field NMR Aims To give an overview of the capability of NMR to answer biological questions To make aware of limitations To give a basic ...
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There is a choice of hydrogen bond partner for each residue. ... Structure class as defined by SCOP or CATH. Folds, as defined by SCOP and CATH ...
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Sequence similarity is observable; homology is a hypothesis based on observation. We want to know whether two ... E.g. SCOP http://scop.mrc-lmb.cam.ac.uk/scop ...
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Scan window 17-25 residues calculate hydrophobicity score. Many false positives ... Hydrophobicity. Use structure fold that best fits profile of parameters. Ab ...
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Title: Finding Patterns in Protein Sequence and Structure Author: mathbio Last modified by: heringa Created Date: 6/9/2002 12:55:37 AM Document presentation format
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Sue Lamont (An Sci, ISU) Integrated genomic approaches to enhance host ... hydrophobicity. contact matrix. Yungok Ihm. i. j. 1. N. Template Structure. Contact Energy ...
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Here we consider the use of Bioinformatics tools rather than their design and construction ... comprehensive range of bioinformatics tools for sequence ...
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a helix = A helical structure, whose chain coils tightly as a right ... Ammonium thioglycolate (alkaline) pH 9.0-10. Glycerylmonothioglycolate (acid) pH 6.5-8.2 ...
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Thanks to Drena Dobbs for many borrowed & modified PPTs ... For continuous output, often use a sigmoid: 0. 1/2. 1. 0. The perceptron ...
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Title: PowerPoint Presentation Author: heringa Last modified by: heringa Created Date: 2/20/2003 6:08:47 PM Document presentation format: Custom Company
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