fragment based computational protein design with cost
play

Fragment-based Computational Protein Design with Cost Function - PowerPoint PPT Presentation

May 26, 2023 •211 likes •257 views

Fragment-based Computational Protein Design with Cost Function Network David Simoncini, Sophie Barbe and Thomas Schiex Math ematiques et Informatique appliqu ees de Toulouse, INRA Simoncini & Barbe & Schiex Fragment-based CPD with

  1. Fragment-based Computational Protein Design with Cost Function Network David Simoncini, Sophie Barbe and Thomas Schiex Math´ ematiques et Informatique appliqu´ ees de Toulouse, INRA Simoncini & Barbe & Schiex Fragment-based CPD with CFN

  2. Background PhD. Thesis, Computer Science University of Nice-Sophia Antipolis, France Selective pressure in cellular evolutionary algorithms Postdoctoral fellowship Zhang IRU, RIKEN, Japan Fragment-based protein structure prediction Computational protein design Simoncini & Barbe & Schiex Fragment-based CPD with CFN

  3. Computational protein design and cost function networks CPD as a cost function network Interactions can be decomposed as a sum of one-body and two-body energy terms. n n − 1 � E ( x r 1 � � E ( x r 1 i , y r 2 E S = i ) + j ) i =1 i =1 j > i Simoncini & Barbe & Schiex Fragment-based CPD with CFN

  4. Fragment-based approach Covering of a protein with fragments Simoncini & Barbe & Schiex Fragment-based CPD with CFN

Recommend

An Efficient Parallel Algorithm for Accelerating Computational Protein Design 1 Institute for

An Efficient Parallel Algorithm for Accelerating Computational Protein Design 1 Institute for

An Efficient Parallel Algorithm for Accelerating Computational Protein Design 1 Institute for Interdisciplinary Information Sciences Tsinghua University 2 Department of Computer Science, Department of Biochemistry Duke University Jul, 2014

1.12k views • 78 slides
Accurate prediction for atomic-level protein design and its application in diversifying the

Accurate prediction for atomic-level protein design and its application in diversifying the

Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space Pablo Gainza CPS 296: Topics in Computational Structural Biology Department of Computer Science Duke University 1 Outline

672 views • 65 slides
Computational Protein Design Using AND/OR Branch-and-Bound Search Yichao Zhou Yuexing Zhou

Computational Protein Design Using AND/OR Branch-and-Bound Search Yichao Zhou Yuexing Zhou

Computational Protein Design Using AND/OR Branch-and-Bound Search Yichao Zhou Yuexing Zhou Jianyang Zeng Institute for Interdisciplinary Information Sciences Tsinghua University Apr, 2015 Yichao Zhou, Yuexing Zhou, Jianyang Zeng

654 views • 54 slides
CAPSID Computational Algorithms for Protein Structures and Interactions David Ritchie + Isaure

CAPSID Computational Algorithms for Protein Structures and Interactions David Ritchie + Isaure

CAPSID Computational Algorithms for Protein Structures and Interactions David Ritchie + Isaure Chauvot de Beauch ene Inria Nancy Grand Est Structural Bioinformatics Tools and Techniques In-House Software Hex protein docking by

344 views • 23 slides
Protein Docking and 3D Ligand-Based Virtual Screening Modeling Protein Flexibility Using Elastic

Protein Docking and 3D Ligand-Based Virtual Screening Modeling Protein Flexibility Using Elastic

Protein Docking and 3D Ligand-Based Virtual Screening Modeling Protein Flexibility Using Elastic Network Models ENMs assume protein atoms (often just CAs) are coupled via a harmonic potential: Part 2 i<j C ( d ij d 0 ij ) 2 V = H ij

899 views • 10 slides
Cap6 Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and

Cap6 Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and

Cap6 Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and implementation too Adaptado dos slides da editora por Mario Crtes IC/Unicamp Goals Correctness High Performance Minimal Hardware

690 views • 58 slides
TOWARDS HOLISTIC BIM-BASED BUILDING DESIGN APPLYING COMPUTATIONAL APPROACHES TO ENHANCE

TOWARDS HOLISTIC BIM-BASED BUILDING DESIGN APPLYING COMPUTATIONAL APPROACHES TO ENHANCE

EKATERINA PETROVA TOWARDS HOLISTIC BIM-BASED BUILDING DESIGN APPLYING COMPUTATIONAL APPROACHES TO ENHANCE SUSTAINABLE DESIGN PRACTICES DANVAK DAGEN 2018, PROFESSOR P. OLE FANGERS FORSKNINGSLEGAT ABOUT ME Feb 2014 - Feb 2016: MSc in Technology in

661 views • 31 slides
Protein design Chris Bystroff Biology 12 Apr 2016 1 Protein folding/ protein design folding

Protein design Chris Bystroff Biology 12 Apr 2016 1 Protein folding/ protein design folding

Protein design Chris Bystroff Biology 12 Apr 2016 1 Protein folding/ protein design folding design structure sequence Sequence space maps to structure space sequence families fold space Structure prediction is "many-to-one".

905 views • 38 slides
Collaboration-based Function Prediction in Protein-Protein Interaction networks Hossein Rahmani

Collaboration-based Function Prediction in Protein-Protein Interaction networks Hossein Rahmani

Collaboration-based Function Prediction in Protein-Protein Interaction networks Hossein Rahmani Joint work with: Hendrik Blockeel, Andreas Bender October 2010 Hossein Rahmani (Leiden University) October 2010 1 / 28 Protein-Protein

435 views • 28 slides
Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and

Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and

Snoop-based Multiprocessor Design Design Goals Performance and cost depend on design and implementation too Goals Correctness High Performance Minimal Hardware Often at odds High Performance => multiple outstanding low-level

1.51k views • 57 slides
Protein Gaussian Image (PGI): a protein structural representa6on

Protein Gaussian Image (PGI): a protein structural representa6on

Protein Gaussian Image (PGI): a protein structural representa6on based on the spa6al a:tude of secondary structure Virginio Cantoni, Department of Computer

277 views • 12 slides
11. Arrays 11- 1 (2) Array Property Fragment of T A Decidable fragment of T A that includes

11. Arrays 11- 1 (2) Array Property Fragment of T A Decidable fragment of T A that includes

11. Arrays 11- 1 (2) Array Property Fragment of T A Decidable fragment of T A that includes quantifiers Array property A -formula of form i . F [ i ] G [ i ] , where i is a list of variables. index guard F [ i ]: iguard

1.19k views • 21 slides
BugBuster: BugBuster: Computational design of a bacterial Computational design of a bacterial

BugBuster: BugBuster: Computational design of a bacterial Computational design of a bacterial

BugBuster: BugBuster: Computational design of a bacterial Computational design of a bacterial biosensor biosensor 2008 Newcastle University iGEM team M. Aylward, R. Chalder, N. Nielsen-Dzumhur, M. Taschuk , J. Thompson & M. Wappett

618 views • 19 slides
1 Method Outline Fragment Matching Fragment Extraction Individual Correspondence

1 Method Outline Fragment Matching Fragment Extraction Individual Correspondence

Overview (1) The major goal of image segmentation is to identify structures in the image that are likely to Class-Specific, Top-Down correspond to scene objects Classic image-based segmentation methods use Segmentation continuity of

523 views • 3 slides
Gene regulation, protein networks and disease a computational perspective Ron Shamir School

Gene regulation, protein networks and disease a computational perspective Ron Shamir School

Gene regulation, protein networks and disease a computational perspective Ron Shamir School of Computer Science Tel Aviv University CPM Helsinki July 3 2012 1 1 Outline Finding regulatory motifs I, II, III Utilizing

923 views • 41 slides
Low Cost Microwave Radiometer WP 2600 Design of a Low Cost Radiometer Thomas Rose Radiometer

Low Cost Microwave Radiometer WP 2600 Design of a Low Cost Radiometer Thomas Rose Radiometer

Low Cost Microwave Radiometer WP 2600 Design of a Low Cost Radiometer Thomas Rose Radiometer Physics GmbH (RPG) Susanne Crewell Meteorological Institute Bonn Madr id, 16 Dezember 2002 1 I ntroduction Ground-based microwave radiometer are

266 views • 14 slides
Computational Methods in Protein Structure Prediction C.A. Floudas Department of Chemical

Computational Methods in Protein Structure Prediction C.A. Floudas Department of Chemical

P ERSPECTIVE Computational Methods in Protein Structure Prediction C.A. Floudas Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263; telephone: 1-609-258-4595; fax: 1-609-258-0211; e-mail:

87 views • 7 slides
Protein Docking and 3D Ligand-Based Virtual Screening Schedule Lecture 1 Rigid Body

Protein Docking and 3D Ligand-Based Virtual Screening Schedule Lecture 1 Rigid Body

Protein Docking and 3D Ligand-Based Virtual Screening Schedule Lecture 1 Rigid Body Protein Docking Part 1 Introduction / Motivation Protein Docking and the CAPRI Blind Docking Experiment The Hex Spherical Polar Fourier

394 views • 12 slides
Design of an energy efficient and low cost trap for Olive fly monitoring using a ZigBee based

Design of an energy efficient and low cost trap for Olive fly monitoring using a ZigBee based

Design of an energy efficient and low cost trap for Olive fly monitoring using a ZigBee based Wireless Sensor Network Alorda, B. (1) , Valds, F. (1) , Mas, B. (1) , Leza, M. (2) , Almenar, L. (2) , Feliu, J. (3) , Ruiz, M. (3) , Miranda, M.A. (2)

146 views • 3 slides
The Fragment Shader CS418 Computer Graphics John C. Hart Fragment Pipeline Rasterization Model

The Fragment Shader CS418 Computer Graphics John C. Hart Fragment Pipeline Rasterization Model

The Fragment Shader CS418 Computer Graphics John C. Hart Fragment Pipeline Rasterization Model Vertex Clip Clip & Window Viewport Coords W2V Interpolation Coords Shader Coords Divide Coords Depth Fragment Pixels Fragments

92 views • 8 slides
February 21, 2006 Guha Jayachandran (guha@stanford.edu), CS379A Protein Design n Determine amino

February 21, 2006 Guha Jayachandran (guha@stanford.edu), CS379A Protein Design n Determine amino

1. Protein Design 2. ADME and Toxicity February 21, 2006 Guha Jayachandran (guha@stanford.edu), CS379A Protein Design n Determine amino acid sequence that will fold into a given three dimensional structure n Maybe even that will have given

307 views • 10 slides
Computational Systems Biology TUM WS 2010/11 Lecture 4: Protein Structure and Disorder in

Computational Systems Biology TUM WS 2010/11 Lecture 4: Protein Structure and Disorder in

Computational Systems Biology TUM WS 2010/11 Lecture 4: Protein Structure and Disorder in Complete Genomes 2010-11-11 Dr. Arthur Dong How To Read A Paper Focus: Technical details or the big picture? Within the paper: What's the whole

414 views • 23 slides
Linear Scaling Three Dimensional Fragment Method for Large Scale Electronic Structure

Linear Scaling Three Dimensional Fragment Method for Large Scale Electronic Structure

Linear Scaling Three Dimensional Fragment Method for Large Scale Electronic Structure Calculations Lin-Wang Wang 1,2 , Byounghak Lee 1 , Zhengji Zhao 2 , Hongzhang Shan 1,2 , Juan Meza 1 , David Bailey 1 , Erich Strohmaier 1,2 1) Computational

475 views • 29 slides
Similar code fragment A code fragment that has similar part to it in source code

Similar code fragment A code fragment that has similar part to it in source code

Similar code fragment A code fragment that has similar part to it in source code introduced in source code because of various reasons. e.g. copy-and-paste makes software maintenance difficult. It is necessary to It is

488 views • 9 slides

More recommend