Improving De novo Protein Structure Prediction using Contact Maps Information
|
|
- Suzanna Ashlie Weaver
- 5 years ago
- Views:
Transcription
1 CIBCB 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology Improving De novo Protein Structure Prediction using Contact Maps Information Karina Baptista dos Santos PhD student in Computational Modeling National Laboratory for Scientific Computing (LNCC) Petrópolis, RJ - Brazil
2 Introduction Protein Structure Prediction (PSP) have a large potentital for biotechnological applications MQTVLKKRKKSGYGYIPD IADIRDFSYTPEKSVIAA LPPKVDLTPSFQVYDQGR IGSCTANALAAAIQFERI HDKQSPEFIPSRLFI Protein Function o Can provide essential clues to understanding diseases o Allows the creation of new proteins and the development of new drugs 2
3 Introduction CASP (Critical Assessment of Techniques for Protein Structure Prediction) o 12th CASP ( ) o Assess the state of the art of protein structure prediction methods Evaluation via process of blind prediction o Progress in PSP methodologies Use of protein contact maps in the search of native conformation o Highlight where the future effort may be focused Proceedings of the National Academy of Sciences pages , 30 NOV
4 Introduction Protein Contact Maps CASP10, CASP11 and CASP12 o A minimalist representation of the 3D protein structure. o Two residues in a protein are in contact if the Euclidean distance between their Cβ atoms (Cα for Glycine) is at most some threshold value, usually 8Å. Cβ i Cβ j 8.0Å Proteins: Structure, Function, and Bioinformatics pages 84-97, 16 OCT 2013 DOI: /prot
5 Introduction Protein Contact Maps prediction Residue covariation analysis o Sufficiently large number of homologous proteins (MSA) Which residue pairs are most likely to be in contact? Which residue pairs are important to be maintained by evolution? MSA inference Contact in 3D covariation These contacts are not template! Contact Map Precision threshold [0, 1] Probability of such residues being in contact Plos One, v.6, n.12 page e28766, 7 DEC 2011 DOI: /prot
6 Introduction Protein Contact Maps prediction o MetaPSICOV 1 (the CASP11 winner) Stage 1 Classic contact prediction features 3 three coevolution-based methods PSICOV, mfdca-free Contact and CCMpred Infer correlations signals in MSA Stage 2 Fill in the gaps in contact map and remove outliers (Filter) Hydrogen bonds patterns between residues in contact 1 Kosciolek, Tomasz, and David T. Jones. "Accurate contact predictions using covariation techniques and machine learning." Proteins: Structure, Function, 6 and Bioinformatics (2015).
7 Objectives Develop a strategy to use the information of protein contact maps in the GAPF PSP program Contact Map Term a new term of the GAPF Fitness Function Assess the predictive information capacity of the contact maps provided by MetaPSICOV Stage 1 7
8 Methods GAPF 2, 3 - Genetic Algorithm for Protein Folding o Phenotypic crowding-based steady-state genetic algorithm o Candidate solutions are encoded by the backbone dihedral angles o Coarse-Grained representation for the side chain atoms 2 GAPF - Custódio, F. L.. Algoritmos Genéticos para Predição Ab Initio de Estrutura de Proteínas. Laboratório Nacional de Computação Científica Custódio, Fábio Lima, Helio J. C. Barbosa, and Laurent Emmanuel Dardenne. A Multiple Minima Genetic Algorithm for Protein Structure Prediction. Applied Soft Computing Journal 15:
9 Methods GAPF - Genetic Algorithm for Protein Folding o Protein Fragment Libraries Profrager 4 Fragment Structure Protein Model o Secondary Structure Prediction PSIPRED 5 4 Trevizani, R., Custódio, F.L., dos Santos, K.B., and Dardenne, L.E. Critical Features of Fragment Libraries for Protein Structure Prediction. PLOS ONE, vol.12, no.1, pp.1-22, Jones, D.t., Protein secondary structure prediction based on position specific scoring matrices. Journal of molecular biology, vol.292, no2, pp ,1999.
10 Methods GAPF - Fitness Function 7 o Based on the energy from the interaction between the atoms of the protein Dihedral potential (from Gromos96 force field); Atomic repulsive term; Hydrophobic compaction term; 4 Hydrogen bond terms Hydrogen bonds 1a Rocha, Gregório Kappaun. Desenvolvimento de Metodologias Para Predição de Estruturas de Proteínas Independente de Moldes. Laboratório Nacional de Computação Científica
11 Methods Contact Map Term Distance constraints λ = Contribution value add to the predicted model energy γ = Precision threshold associated with the probability of such residues being in contact σ(i, j) = Euclidean distance between Cβ atoms of residues i and j o The more residues are respecting the distance constrainsts, the greater the contribution to the fitness function 11
12 Methods Test Set Experimentally determined 3D structures 3FIL 56 residues T0773-D1 67 residues (PDB 2N2U) T0820-D1 90 residues T0769-D1 97 residues (PDB 2MQ8) T0766-D1 108 residues (PDB 4Q53) 12
13 Methods Contact Maps o Native Map All residues pairs found in native structure (PDB file) Precision threshold (PT) = 1.0 R1 R2 d min d max PT
14 Methods Contact Maps o Filtered Map Only the residues pairs predicted by MetaPSICOV Stage1 that are present in the Native Map. Precision threshold (PT) = MetaPSICOV Predicted value R1 R2 d min d max PT
15 Methods Contact Maps o Filtered Map Only the residues pairs predicted by MetaPSICOV Stage1 that are present in the Native Map. Precision threshold (PT) = MetaPSICOV Predicted value R1 R2 d min d max PT Native X Filtered Same Residues / Different Precision Threshold 15
16 Filtered Map - Precision threshold profile
17 Native x False contacts in the MetaPSICOV predicted map Contact Pairs Filter native contacts from predicted map Great challenge filA T0773-D1 T0820-D1 T0769-D1 T0766-D1 All MetaPSICOV Stage1 contacts Native contacts o No method described is able to do this selection efficiently Precision threshold above some value (e.g. 0.5, 0.4 ) Number of contacts associated with the sequence length ( e.g., L/5, L/2 ) 17
18 Results Impact of the use of Contact Maps o 4000 models predicted by GAPF Best of All Models Predicted Top5 Best Energy Models o RMSD 4.0Å Good predictions 18
19 Results Impact of the use of Contact Maps o 4000 models predicted by GAPF Best of All Models Predicted T0820-D1 Top5 Best Energy Models 6Å >10Å o RMSD 4.0Å Good predictions 19
20 Results Satisfied contact does not mean correct contact! Best of All Top 5 Best Energy Native Map 60% 65% Filtered Map 48% 44% Cβ i Cβ j 8.0Å Native Structure Cβ- Cβ = 7.71 Å Model Cβ- Cβ = 4.23 Å 20
21 Results RMSD (Å) RMSD (Å) RMSD (Å) RMSD x Energy (Native Map) The greatest contribution to GAPF 3FIL T0773-D1 Energy (Kcal/mol) Energy (Kcal/mol) T0820-D1 Energy (Kcal/mol) 21
22 Results RMSD x Energy (Standard Procotol) o Difficult to select the best structure model methodology to select decoys 3FIL T0820-D1 22
23 Results T0820-D1 - Summary of improvements GAFP_St GAFP_Cm Native map GAFP_Cm Filtered map Best of All Models RMSD = 9.60 Å GDT = % RMSD = 3.19 Å GDT = % RMSD = 3.73 Å GDT = % Top 5 Best Energy Models RMSD = Å GDT = % RMSD = 3.61 Å GDT = % RMSD = 3.65 Å GDT = % Experimental Structure Model predicted by GAPF program 23
24 Conclusions Contact Map in the form of Distance Constrains Useful Strategy for PSP Naive Potential Properly combined with GAPF fitness function Predictors give probability for all possible residue-residue contacts o Lack of full confidence in the prediction of the contacts Development of strategies to filter and enhance contact maps o Which contacts are most valuable for PSP 24
25 Acknowledgment Thank you! 25
Contact map guided ab initio structure prediction
Contact map guided ab initio structure prediction S M Golam Mortuza Postdoctoral Research Fellow I-TASSER Workshop 2017 North Carolina A&T State University, Greensboro, NC Outline Ab initio structure prediction:
More informationCMPS 6630: Introduction to Computational Biology and Bioinformatics. Tertiary Structure Prediction
CMPS 6630: Introduction to Computational Biology and Bioinformatics Tertiary Structure Prediction Tertiary Structure Prediction Why Should Tertiary Structure Prediction Be Possible? Molecules obey the
More informationCMPS 3110: Bioinformatics. Tertiary Structure Prediction
CMPS 3110: Bioinformatics Tertiary Structure Prediction Tertiary Structure Prediction Why Should Tertiary Structure Prediction Be Possible? Molecules obey the laws of physics! Conformation space is finite
More informationDesign of a Novel Globular Protein Fold with Atomic-Level Accuracy
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker Presented by Kate Stafford 4 May 05 Protein
More informationProtein Structure Prediction, Engineering & Design CHEM 430
Protein Structure Prediction, Engineering & Design CHEM 430 Eero Saarinen The free energy surface of a protein Protein Structure Prediction & Design Full Protein Structure from Sequence - High Alignment
More informationPresenter: She Zhang
Presenter: She Zhang Introduction Dr. David Baker Introduction Why design proteins de novo? It is not clear how non-covalent interactions favor one specific native structure over many other non-native
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/309/5742/1868/dc1 Supporting Online Material for Toward High-Resolution de Novo Structure Prediction for Small Proteins Philip Bradley, Kira M. S. Misura, David Baker*
More informationHomology Modeling. Roberto Lins EPFL - summer semester 2005
Homology Modeling Roberto Lins EPFL - summer semester 2005 Disclaimer: course material is mainly taken from: P.E. Bourne & H Weissig, Structural Bioinformatics; C.A. Orengo, D.T. Jones & J.M. Thornton,
More informationProtein structure prediction. CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror
Protein structure prediction CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror 1 Outline Why predict protein structure? Can we use (pure) physics-based methods? Knowledge-based methods Two major
More informationProtein structure prediction. CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror
Protein structure prediction CS/CME/BioE/Biophys/BMI 279 Oct. 10 and 12, 2017 Ron Dror 1 Outline Why predict protein structure? Can we use (pure) physics-based methods? Knowledge-based methods Two major
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationProtein Structure Prediction
Protein Structure Prediction Michael Feig MMTSB/CTBP 2009 Summer Workshop From Sequence to Structure SEALGDTIVKNA Folding with All-Atom Models AAQAAAAQAAAAQAA All-atom MD in general not succesful for real
More informationStatistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics
Statistical Machine Learning Methods for Bioinformatics IV. Neural Network & Deep Learning Applications in Bioinformatics Jianlin Cheng, PhD Department of Computer Science University of Missouri, Columbia
More informationAb-initio protein structure prediction
Ab-initio protein structure prediction Jaroslaw Pillardy Computational Biology Service Unit Cornell Theory Center, Cornell University Ithaca, NY USA Methods for predicting protein structure 1. Homology
More informationMolecular Modeling. Prediction of Protein 3D Structure from Sequence. Vimalkumar Velayudhan. May 21, 2007
Molecular Modeling Prediction of Protein 3D Structure from Sequence Vimalkumar Velayudhan Jain Institute of Vocational and Advanced Studies May 21, 2007 Vimalkumar Velayudhan Molecular Modeling 1/23 Outline
More informationProtein Structure Determination
Protein Structure Determination Given a protein sequence, determine its 3D structure 1 MIKLGIVMDP IANINIKKDS SFAMLLEAQR RGYELHYMEM GDLYLINGEA 51 RAHTRTLNVK QNYEEWFSFV GEQDLPLADL DVILMRKDPP FDTEFIYATY 101
More informationBuilding 3D models of proteins
Building 3D models of proteins Why make a structural model for your protein? The structure can provide clues to the function through structural similarity with other proteins With a structure it is easier
More informationHomology Modeling (Comparative Structure Modeling) GBCB 5874: Problem Solving in GBCB
Homology Modeling (Comparative Structure Modeling) Aims of Structural Genomics High-throughput 3D structure determination and analysis To determine or predict the 3D structures of all the proteins encoded
More informationAlpha-helical Topology and Tertiary Structure Prediction of Globular Proteins Scott R. McAllister Christodoulos A. Floudas Princeton University
Alpha-helical Topology and Tertiary Structure Prediction of Globular Proteins Scott R. McAllister Christodoulos A. Floudas Princeton University Department of Chemical Engineering Program of Applied and
More informationA genetic algorithm for the ligand-protein docking problem
Research Article Genetics and Molecular Biology, 27, 4, 605-610 (2004) Copyright by the Brazilian Society of Genetics. Printed in Brazil www.sbg.org.br A genetic algorithm for the ligand-protein docking
More informationAB initio protein structure prediction or template-free
IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 10, NO. X, XXXXXXX 2013 1 Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction
More informationProcheck output. Bond angles (Procheck) Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics.
Structure verification and validation Bond lengths (Procheck) Introduction to Bioinformatics Iosif Vaisman Email: ivaisman@gmu.edu ----------------------------------------------------------------- Bond
More informationPrediction and refinement of NMR structures from sparse experimental data
Prediction and refinement of NMR structures from sparse experimental data Jeff Skolnick Director Center for the Study of Systems Biology School of Biology Georgia Institute of Technology Overview of talk
More informationFrancisco Melo, Damien Devos, Eric Depiereux and Ernest Feytmans
From: ISMB-97 Proceedings. Copyright 1997, AAAI (www.aaai.org). All rights reserved. ANOLEA: A www Server to Assess Protein Structures Francisco Melo, Damien Devos, Eric Depiereux and Ernest Feytmans Facultés
More informationA new prediction strategy for long local protein. structures using an original description
Author manuscript, published in "Proteins Structure Function and Bioinformatics 2009;76(3):570-87" DOI : 10.1002/prot.22370 A new prediction strategy for long local protein structures using an original
More informationTemplate Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Associate Professor Computer Science Department Informatics Institute University of Missouri, Columbia 2013 Protein Energy Landscape & Free Sampling
More informationCAP 5510 Lecture 3 Protein Structures
CAP 5510 Lecture 3 Protein Structures Su-Shing Chen Bioinformatics CISE 8/19/2005 Su-Shing Chen, CISE 1 Protein Conformation 8/19/2005 Su-Shing Chen, CISE 2 Protein Conformational Structures Hydrophobicity
More informationProtein structure analysis. Risto Laakso 10th January 2005
Protein structure analysis Risto Laakso risto.laakso@hut.fi 10th January 2005 1 1 Summary Various methods of protein structure analysis were examined. Two proteins, 1HLB (Sea cucumber hemoglobin) and 1HLM
More informationCMPS 6630: Introduction to Computational Biology and Bioinformatics. Structure Comparison
CMPS 6630: Introduction to Computational Biology and Bioinformatics Structure Comparison Protein Structure Comparison Motivation Understand sequence and structure variability Understand Domain architecture
More informationThe typical end scenario for those who try to predict protein
A method for evaluating the structural quality of protein models by using higher-order pairs scoring Gregory E. Sims and Sung-Hou Kim Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory,
More informationFinding Similar Protein Structures Efficiently and Effectively
Finding Similar Protein Structures Efficiently and Effectively by Xuefeng Cui A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy
More information114 Grundlagen der Bioinformatik, SS 09, D. Huson, July 6, 2009
114 Grundlagen der Bioinformatik, SS 09, D. Huson, July 6, 2009 9 Protein tertiary structure Sources for this chapter, which are all recommended reading: D.W. Mount. Bioinformatics: Sequences and Genome
More informationTemplate Free Protein Structure Modeling Jianlin Cheng, PhD
Template Free Protein Structure Modeling Jianlin Cheng, PhD Professor Department of EECS Informatics Institute University of Missouri, Columbia 2018 Protein Energy Landscape & Free Sampling http://pubs.acs.org/subscribe/archive/mdd/v03/i09/html/willis.html
More informationProtein Structure Prediction
Page 1 Protein Structure Prediction Russ B. Altman BMI 214 CS 274 Protein Folding is different from structure prediction --Folding is concerned with the process of taking the 3D shape, usually based on
More informationHOMOLOGY MODELING. The sequence alignment and template structure are then used to produce a structural model of the target.
HOMOLOGY MODELING Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental
More information) P = 1 if exp # " s. + 0 otherwise
Supplementary Material Monte Carlo algorithm procedures. The Monte Carlo conformational search algorithm has been successfully applied by programs dedicated to finding new folds (Jones 2001; Rohl, Strauss,
More informationPortal. User Guide Version 1.0. Contributors
Portal www.dockthor.lncc.br User Guide Version 1.0 Contributors Diogo A. Marinho, Isabella A. Guedes, Eduardo Krempser, Camila S. de Magalhães, Hélio J. C. Barbosa and Laurent E. Dardenne www.gmmsb.lncc.br
More informationDetecting unfolded regions in protein sequences. Anne Poupon Génomique Structurale de la Levure IBBMC Université Paris-Sud / CNRS France
Detecting unfolded regions in protein sequences Anne Poupon Génomique Structurale de la Levure IBBMC Université Paris-Sud / CNRS France Large proteins and complexes: a domain approach Structural studies
More informationDISCRETE TUTORIAL. Agustí Emperador. Institute for Research in Biomedicine, Barcelona APPLICATION OF DISCRETE TO FLEXIBLE PROTEIN-PROTEIN DOCKING:
DISCRETE TUTORIAL Agustí Emperador Institute for Research in Biomedicine, Barcelona APPLICATION OF DISCRETE TO FLEXIBLE PROTEIN-PROTEIN DOCKING: STRUCTURAL REFINEMENT OF DOCKING CONFORMATIONS Emperador
More informationTemplate-Based Modeling of Protein Structure
Template-Based Modeling of Protein Structure David Constant Biochemistry 218 December 11, 2011 Introduction. Much can be learned about the biology of a protein from its structure. Simply put, structure
More informationFlexPepDock In a nutshell
FlexPepDock In a nutshell All Tutorial files are located in http://bit.ly/mxtakv FlexPepdock refinement Step 1 Step 3 - Refinement Step 4 - Selection of models Measure of fit FlexPepdock Ab-initio Step
More informationProgramme Last week s quiz results + Summary Fold recognition Break Exercise: Modelling remote homologues
Programme 8.00-8.20 Last week s quiz results + Summary 8.20-9.00 Fold recognition 9.00-9.15 Break 9.15-11.20 Exercise: Modelling remote homologues 11.20-11.40 Summary & discussion 11.40-12.00 Quiz 1 Feedback
More informationConformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview
# of Loops, http://dx.doi.org/10.5936/csbj.201302003 CSBJ Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview Yaohang Li a,* Abstract: Accurately modeling protein loops
More informationWeek 10: Homology Modelling (II) - HHpred
Week 10: Homology Modelling (II) - HHpred Course: Tools for Structural Biology Fabian Glaser BKU - Technion 1 2 Identify and align related structures by sequence methods is not an easy task All comparative
More informationTemplate Based Protein Structure Modeling Jianlin Cheng, PhD
Template Based Protein Structure Modeling Jianlin Cheng, PhD Professor Department of EECS Informatics Institute University of Missouri, Columbia 2018 Sequence, Structure and Function AGCWY Cell Protein
More informationProtein Structure Prediction II Lecturer: Serafim Batzoglou Scribe: Samy Hamdouche
Protein Structure Prediction II Lecturer: Serafim Batzoglou Scribe: Samy Hamdouche The molecular structure of a protein can be broken down hierarchically. The primary structure of a protein is simply its
More informationComparative Study of Machine Learning Models in Protein Structure Prediction
Comparative Study of Machine Learning Models in Protein Structure Prediction *Sonal Mishra 1, *Anamika Ahirwar 2 * 1 Computer Science and Engineering Department, Maharana Pratap College of technology Gwalior.
More informationEvolutionary design of energy functions for protein structure prediction
Evolutionary design of energy functions for protein structure prediction Natalio Krasnogor nxk@ cs. nott. ac. uk Paweł Widera, Jonathan Garibaldi 7th Annual HUMIES Awards 2010-07-09 Protein structure prediction
More informationproteins The dual role of fragments in fragmentassembly methods for de novo protein structure prediction
proteins STRUCTURE O FUNCTION O BIOINFORMATICS The dual role of fragments in fragmentassembly methods for de novo protein structure prediction Julia Handl, 1 * Joshua Knowles, 2 Robert Vernon, 3 David
More informationBioinformatics. Macromolecular structure
Bioinformatics Macromolecular structure Contents Determination of protein structure Structure databases Secondary structure elements (SSE) Tertiary structure Structure analysis Structure alignment Domain
More informationBioinformatics: Secondary Structure Prediction
Bioinformatics: Secondary Structure Prediction Prof. David Jones d.jones@cs.ucl.ac.uk LMLSTQNPALLKRNIIYWNNVALLWEAGSD The greatest unsolved problem in molecular biology:the Protein Folding Problem? Entries
More informationExamples of Protein Modeling. Protein Modeling. Primary Structure. Protein Structure Description. Protein Sequence Sources. Importing Sequences to MOE
Examples of Protein Modeling Protein Modeling Visualization Examination of an experimental structure to gain insight about a research question Dynamics To examine the dynamics of protein structures To
More informationMolecular Modeling Lecture 7. Homology modeling insertions/deletions manual realignment
Molecular Modeling 2018-- Lecture 7 Homology modeling insertions/deletions manual realignment Homology modeling also called comparative modeling Sequences that have similar sequence have similar structure.
More informationComputational engineering of cellulase Cel9A-68 functional motions through mutations in its linker region. WT 1TF4 (crystal) -90 ERRAT PROVE VERIFY3D
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 218 Supplementary Material: Computational engineering of cellulase Cel9-68 functional
More informationProtein Structures. 11/19/2002 Lecture 24 1
Protein Structures 11/19/2002 Lecture 24 1 All 3 figures are cartoons of an amino acid residue. 11/19/2002 Lecture 24 2 Peptide bonds in chains of residues 11/19/2002 Lecture 24 3 Angles φ and ψ in the
More informationProtein Structure Prediction
Protein Structure Prediction Michael Feig MMTSB/CTBP 2006 Summer Workshop From Sequence to Structure SEALGDTIVKNA Ab initio Structure Prediction Protocol Amino Acid Sequence Conformational Sampling to
More informationSyllabus of BIOINF 528 (2017 Fall, Bioinformatics Program)
Syllabus of BIOINF 528 (2017 Fall, Bioinformatics Program) Course Name: Structural Bioinformatics Course Description: Instructor: This course introduces fundamental concepts and methods for structural
More informationProtein Modeling Methods. Knowledge. Protein Modeling Methods. Fold Recognition. Knowledge-based methods. Introduction to Bioinformatics
Protein Modeling Methods Introduction to Bioinformatics Iosif Vaisman Ab initio methods Energy-based methods Knowledge-based methods Email: ivaisman@gmu.edu Protein Modeling Methods Ab initio methods:
More informationBioinformatics: Secondary Structure Prediction
Bioinformatics: Secondary Structure Prediction Prof. David Jones d.t.jones@ucl.ac.uk Possibly the greatest unsolved problem in molecular biology: The Protein Folding Problem MWMPPRPEEVARK LRRLGFVERMAKG
More informationProtein Structure Prediction 11/11/05
11/11/05 Protein Structure Prediction & Modeling Bioinformatics Seminars Nov 11 Fri 12:10 BCB Seminar in E164 Lago Building Supertrees Using Distances Steve Willson, Dept of Mathematics http://www.bcb.iastate.edu/courses/bcb691-f2005.html
More informationBioinformatics III Structural Bioinformatics and Genome Analysis Part Protein Secondary Structure Prediction. Sepp Hochreiter
Bioinformatics III Structural Bioinformatics and Genome Analysis Part Protein Secondary Structure Prediction Institute of Bioinformatics Johannes Kepler University, Linz, Austria Chapter 4 Protein Secondary
More informationMulti-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins
Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins Zhong Chen Dept. of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602 Email: zc@csbl.bmb.uga.edu
More informationBasics of protein structure
Today: 1. Projects a. Requirements: i. Critical review of one paper ii. At least one computational result b. Noon, Dec. 3 rd written report and oral presentation are due; submit via email to bphys101@fas.harvard.edu
More informationPROTEIN STRUCTURE PREDICTION II
PROTEIN STRUCTURE PREDICTION II Jeffrey Skolnick 1,2 Yang Zhang 1 Because the molecular function of a protein depends on its three dimensional structure, which is often unknown, protein structure prediction
More informationIntroduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
More informationComputational Molecular Biology (
Computational Molecular Biology (http://cmgm cmgm.stanford.edu/biochem218/) Biochemistry 218/Medical Information Sciences 231 Douglas L. Brutlag, Lee Kozar Jimmy Huang, Josh Silverman Lecture Syllabus
More informationGiri Narasimhan. CAP 5510: Introduction to Bioinformatics. ECS 254; Phone: x3748
CAP 5510: Introduction to Bioinformatics Giri Narasimhan ECS 254; Phone: x3748 giri@cis.fiu.edu www.cis.fiu.edu/~giri/teach/bioinfs07.html 2/15/07 CAP5510 1 EM Algorithm Goal: Find θ, Z that maximize Pr
More informationCan protein model accuracy be. identified? NO! CBS, BioCentrum, Morten Nielsen, DTU
Can protein model accuracy be identified? Morten Nielsen, CBS, BioCentrum, DTU NO! Identification of Protein-model accuracy Why is it important? What is accuracy RMSD, fraction correct, Protein model correctness/quality
More informationPredicting protein contact map using evolutionary and physical constraints by integer programming (extended version)
Predicting protein contact map using evolutionary and physical constraints by integer programming (extended version) Zhiyong Wang 1 and Jinbo Xu 1,* 1 Toyota Technological Institute at Chicago 6045 S Kenwood,
More informationProtein Structure Analysis and Verification. Course S Basics for Biosystems of the Cell exercise work. Maija Nevala, BIO, 67485U 16.1.
Protein Structure Analysis and Verification Course S-114.2500 Basics for Biosystems of the Cell exercise work Maija Nevala, BIO, 67485U 16.1.2008 1. Preface When faced with an unknown protein, scientists
More informationproteins Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field Dong Xu1 and Yang Zhang1,2* 1 Department
More informationDihedral Angles. Homayoun Valafar. Department of Computer Science and Engineering, USC 02/03/10 CSCE 769
Dihedral Angles Homayoun Valafar Department of Computer Science and Engineering, USC The precise definition of a dihedral or torsion angle can be found in spatial geometry Angle between to planes Dihedral
More informationBetter Bond Angles in the Protein Data Bank
Better Bond Angles in the Protein Data Bank C.J. Robinson and D.B. Skillicorn School of Computing Queen s University {robinson,skill}@cs.queensu.ca Abstract The Protein Data Bank (PDB) contains, at least
More informationALL LECTURES IN SB Introduction
1. Introduction 2. Molecular Architecture I 3. Molecular Architecture II 4. Molecular Simulation I 5. Molecular Simulation II 6. Bioinformatics I 7. Bioinformatics II 8. Prediction I 9. Prediction II ALL
More informationPrediction of Protein Backbone Structure by Preference Classification with SVM
Prediction of Protein Backbone Structure by Preference Classification with SVM Kai-Yu Chen #, Chang-Biau Yang #1 and Kuo-Si Huang & # National Sun Yat-sen University, Kaohsiung, Taiwan & National Kaohsiung
More informationProtein Structure Determination from Pseudocontact Shifts Using ROSETTA
Supporting Information Protein Structure Determination from Pseudocontact Shifts Using ROSETTA Christophe Schmitz, Robert Vernon, Gottfried Otting, David Baker and Thomas Huber Table S0. Biological Magnetic
More informationSCOP. all-β class. all-α class, 3 different folds. T4 endonuclease V. 4-helical cytokines. Globin-like
SCOP all-β class 4-helical cytokines T4 endonuclease V all-α class, 3 different folds Globin-like TIM-barrel fold α/β class Profilin-like fold α+β class http://scop.mrc-lmb.cam.ac.uk/scop CATH Class, Architecture,
More informationHIV protease inhibitor. Certain level of function can be found without structure. But a structure is a key to understand the detailed mechanism.
Proteins are linear polypeptide chains (one or more) Building blocks: 20 types of amino acids. Range from a few 10s-1000s They fold into varying three-dimensional shapes structure medicine Certain level
More informationProtein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
More informationProtein Structure Analysis with Sequential Monte Carlo Method. Jinfeng Zhang Computational Biology Lab Department of Statistics Harvard University
Protein Structure Analysis with Sequential Monte Carlo Method Jinfeng Zhang Computational Biology Lab Department of Statistics Harvard University Introduction Structure Function & Interaction Protein structure
More informationDocking. GBCB 5874: Problem Solving in GBCB
Docking Benzamidine Docking to Trypsin Relationship to Drug Design Ligand-based design QSAR Pharmacophore modeling Can be done without 3-D structure of protein Receptor/Structure-based design Molecular
More informationChemical Shift Restraints Tools and Methods. Andrea Cavalli
Chemical Shift Restraints Tools and Methods Andrea Cavalli Overview Methods Overview Methods Details Overview Methods Details Results/Discussion Overview Methods Methods Cheshire base solid-state Methods
More informationReconstruction of Protein Backbone with the α-carbon Coordinates *
JOURNAL OF INFORMATION SCIENCE AND ENGINEERING 26, 1107-1119 (2010) Reconstruction of Protein Backbone with the α-carbon Coordinates * JEN-HUI WANG, CHANG-BIAU YANG + AND CHIOU-TING TSENG Department of
More informationPacking of Secondary Structures
7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary
More informationGoals. Structural Analysis of the EGR Family of Transcription Factors: Templates for Predicting Protein DNA Interactions
Structural Analysis of the EGR Family of Transcription Factors: Templates for Predicting Protein DNA Interactions Jamie Duke 1,2 and Carlos Camacho 3 1 Bioengineering and Bioinformatics Summer Institute,
More informationproteins Comparison of structure-based and threading-based approaches to protein functional annotation Michal Brylinski, and Jeffrey Skolnick*
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Comparison of structure-based and threading-based approaches to protein functional annotation Michal Brylinski, and Jeffrey Skolnick* Center for the Study
More informationproteins Estimating quality of template-based protein models by alignment stability Hao Chen 1 and Daisuke Kihara 1,2,3,4 * INTRODUCTION
proteins STRUCTURE O FUNCTION O BIOINFORMATICS Estimating quality of template-based protein models by alignment stability Hao Chen 1 and Daisuke Kihara 1,2,3,4 * 1 Department of Biological Sciences, College
More informationAssignment 2 Atomic-Level Molecular Modeling
Assignment 2 Atomic-Level Molecular Modeling CS/BIOE/CME/BIOPHYS/BIOMEDIN 279 Due: November 3, 2016 at 3:00 PM The goal of this assignment is to understand the biological and computational aspects of macromolecular
More informationKd = koff/kon = [R][L]/[RL]
Taller de docking y cribado virtual: Uso de herramientas computacionales en el diseño de fármacos Docking program GLIDE El programa de docking GLIDE Sonsoles Martín-Santamaría Shrödinger is a scientific
More informationChemogenomic: Approaches to Rational Drug Design. Jonas Skjødt Møller
Chemogenomic: Approaches to Rational Drug Design Jonas Skjødt Møller Chemogenomic Chemistry Biology Chemical biology Medical chemistry Chemical genetics Chemoinformatics Bioinformatics Chemoproteomics
More informationApril, The energy functions include:
REDUX A collection of Python scripts for torsion angle Monte Carlo protein molecular simulations and analysis The program is based on unified residue peptide model and is designed for more efficient exploration
More informationAll-atom ab initio folding of a diverse set of proteins
All-atom ab initio folding of a diverse set of proteins Jae Shick Yang 1, William W. Chen 2,1, Jeffrey Skolnick 3, and Eugene I. Shakhnovich 1, * 1 Department of Chemistry and Chemical Biology 2 Department
More informationChemical properties that affect binding of enzyme-inhibiting drugs to enzymes
Introduction Chemical properties that affect binding of enzyme-inhibiting drugs to enzymes The production of new drugs requires time for development and testing, and can result in large prohibitive costs
More informationSupplementing information theory with opposite polarity of amino acids for protein contact prediction
Supplementing information theory with opposite polarity of amino acids for protein contact prediction Yancy Liao 1, Jeremy Selengut 1 1 Department of Computer Science, University of Maryland - College
More informationGeneralized Pattern Search Algorithm for Peptide Structure Prediction
4988 Biophysical Journal Volume 95 September 2008 4988 4999 Generalized Pattern Search Algorithm for Peptide Structure Prediction Giuseppe Nicosia and Giovanni Stracquadanio Department of Mathematics and
More informationLOCAL MINIMA HOPPING ALONG THE PROTEIN ENERGY SURFACE
LOCAL MINIMA HOPPING ALONG THE PROTEIN ENERGY SURFACE by Brian Olson A Thesis Submitted to the Graduate Faculty of George Mason University In Partial Fulfillment of The Requirements for the Degree of Master
More informationProtein quality assessment
Protein quality assessment Speaker: Renzhi Cao Advisor: Dr. Jianlin Cheng Major: Computer Science May 17 th, 2013 1 Outline Introduction Paper1 Paper2 Paper3 Discussion and research plan Acknowledgement
More informationNeural Networks for Protein Structure Prediction Brown, JMB CS 466 Saurabh Sinha
Neural Networks for Protein Structure Prediction Brown, JMB 1999 CS 466 Saurabh Sinha Outline Goal is to predict secondary structure of a protein from its sequence Artificial Neural Network used for this
More information1-D Predictions. Prediction of local features: Secondary structure & surface exposure
1-D Predictions Prediction of local features: Secondary structure & surface exposure 1 Learning Objectives After today s session you should be able to: Explain the meaning and usage of the following local
More informationProtein Structure Prediction on GPU: a Declarative Approach in a Multi-agent Framework
Protein Structure Prediction on GPU: a Declarative Approach in a Multi-agent Framework Federico Campeotto (1),(2) Agostino Dovier (2) Enrico Pontelli (1) campe8@nmsu.edu agostino.dovier@uniud.it epontell@cs.nmsu.edu
More information