Protein Structure and Function: Applications of Bioinformatics Methods - John Rigden 2014
ab initio Protein Structure Prediction
Ab initio protein structure prediction
Energy functions
ab initio Protein Structure Prediction
Energy Functions
Combination of Empirical Energy Functions and Fragment Assembly
Ab Initio Protein Structure Prediction
Ab initio Protein Structure Prediction
Ab Initio Protein Structure Prediction
Ab initio Protein Structure Prediction
Ab initio protein structure prediction
Ab Initio Protein Structure Prediction
Model Selection
Structure-Sequence Compatibility Function
Clustering of Structural Models
ab initio Protein Structure Prediction
Fold Recognition
Fold recognition
The importance of "blind" tests: The CASP competition
Fold Recognition
Ab Initio Structure Prediction and Homology Modeling
On terminology: “threading” and “fold recognition”
Fold recognition
Fold Recognition
Remote Homology Detection Without Gaps
Remote Homology Detection Without Alignment
Utilization of Predicted Structural Properties
Fold recognition
Detection of remote homology without alignment
Sequence profiles and Hidden Markov Models
Fold Recognition
Remote Homology Detection Without Alignment
Classification of Fold Types and the Support Vector Machine Method
Detection of Remote Homology without Alignment
Alignment Accuracy, Model Quality, and Statistical Significance
Alignment Generation Algorithms and Scoring
Evaluation of Statistical Significance
Web Tools for Fold Recognition
Comparative Protein Structure Modeling
Introduction
Sequences, Structures, and Structural Genomics
Protein Structure Prediction Methods
Steps in Comparative Protein Structure Modeling
Searching for Structures Potentially Related to the Target
Stages of Comparative Protein Structure Modeling
Steps in Comparative Protein Structure Modeling
Sequence-to-Structure Alignment
Efficiency of Comparative Modeling Methods
Applications of Comparative Modeling
Comparative Modeling and the Protein Structure Research Project
Prediction of membrane protein structure
Structural classes
Prediction of Membrane Protein Structure
Structural Classes
Prediction of membrane protein structure
Characteristics of membrane protein crystallization
Prediction of Membrane Protein Structure
Prediction of Transmembrane Protein Topology
Membrane Protein Structure Prediction
Genome-Wide Association Studies
Prediction of Membrane Protein Structure
Datasets, Homology, Accuracy, and Cross-Validation
Prediction of Spatial Structure
Future Prospects for Membrane Protein Structure Prediction Methods
Bioinformatics methods for studying the structure and function of intrinsically disordered proteins
The concept of protein disorder
Bioinformatics methods for studying the structure and functions of disordered proteins
Properties of IDP sequences
Unusual amino acid composition of IDPs
Bioinformatics Methods for Studying the Structure and Function of Intrinsically Disordered Proteins
Properties of IDP Sequences
Bioinformatics Methods for Studying the Structure and Function of Unordered Proteins
Low Sequence Complexity and Disorder
Bioinformatics methods for studying the structure and function of disordered proteins
Disorder prediction
Prediction of low-complexity regions
Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Disorder Prediction
Propensity-Based Prediction Methods
Bioinformatics Methods for Studying the Structure and Functions of Disordered Proteins
Prediction Methods Based on the Absence of Well-Defined Secondary Structure
Bioinformatics methods for studying the structure and function of disordered proteins
Disorder prediction
Bioinformatics Methods for Studying the Structure and Function of Unordered Proteins
Prediction of Disorder
Prediction Based on Contact Potentials
Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Disorder Prediction
A reduced alphabet is sufficient for disorder prediction
Bioinformatics methods for studying the structure and function of disordered proteins
Prediction of disorder
Comparison of disorder prediction methods
Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Functional Classification of IDPs
Functional Classification of IDPs Based on Gene Ontology
Bioinformatics Methods for Studying the Structure and Functions of Disordered Proteins
Classification of IDPs Based on Mechanism of Action
Bioinformatics methods for studying the structure and function of disordered proteins
Functional classification of IDPs
Structural elements of IDPs associated with functioning
Bioinformatics methods for studying the structure and functions of disordered proteins
Prediction of IDP functions
Correlation of disorder model and function
Bioinformatics methods for studying the structure and function of disordered proteins
Prediction of short recognition motifs in IDPs
Bioinformatics Methods for Studying the Structure and Function of Disordered Proteins
Prediction of IDP Functions
Combining Sequence and Disorder Information: Phosphorylation Sites and CaM-Binding Motifs
Limitations of IDP Function Prediction Methods
Sequence-Function Independence and Ambiguity
Bioinformatics methods for studying the structure and function of disordered proteins
Bioinformatics Methods for Studying the Structure and Functions of Disordered Proteins
Functional diversity in packing elements and superfamilies
Functional Diversity in Packing Elements and Superfamilies
From Fold to Function
Functional Diversity in Packing Motifs and Superfamilies
From Folding to Function
Relationship Between Folding Patterns and Function Prediction
Functional diversity in packing elements and superfamilies
Functional diversity of homologous proteins
Diversity of functions in homologous proteins
Evolution of protein superfamilies
Functional Diversity in Packing Elements and Superfamilies
Functional Diversity of Homologous Proteins
Functional Divergence during Protein Evolution
Functional diversity in packing motifs and superfamilies
Functional Diversity in Packaging Motifs and Superfamilies
Predicting Protein Function from Surface Properties
Methods of Surface Representation
Surface Representation Methods
Molecular Surface (Solvent-Excluded Surface)
Prediction of protein function based on its surface properties
Methods of surface representation
Predicting Protein Function from Surface Properties
Surface Properties
Protein Function Prediction via Surface Properties
Protein Function Prediction Based on Surface Properties
Prediction of protein function based on its surface properties
Prediction of functions by surface properties
Protein Function Prediction Based on Surface Properties
Function Prediction from Surface Properties
Prediction of Protein Function from Surface Properties
Functional Prediction Based on Surface Properties
Predicting protein function from surface properties
Function prediction from surface properties
Combining surface properties for function prediction
Prediction of protein function based on its surface properties
Ligand-protein interaction
Properties of ligand-protein interactions
Prediction of Protein Function from Surface Properties
Ligand-Protein Interaction
Prediction of Active Site Location
Prediction of protein function from its surface properties
Ligand-protein interaction
Prediction of drug sensitivity
Annotation of ligand-binding sites
Prediction of Protein Function from Surface Properties
Protein-Protein Interface
Properties of the Protein-Protein Interface
Hot Spots in Protein Interfaces
Prediction of protein function based on surface properties
Protein-protein interface
Prediction of interface location
Predicting Protein Function from Surface Properties
Prediction of Protein Function from Its Surface Properties
Spatial Motifs
Structural Motifs
Spatial Motifs
Structural Motifs: Definition and Scope
Structural Motifs
Overview of Methods
Spatial Motifs
Identification and Selection of Motifs
Spatial motifs
Specific methods
Structural motifs
Spatial Motifs
Similar Methods
Point-Surface Hybrid Descriptions
Spatial motifs
Similar methods
Structural Motifs
Application of Molecular Docking in Function Annotation
Spatial Motifs
Structural Motifs
Protein Dynamics: From Structure to Function
Molecular Dynamics Calculations
Limitations and Enhanced Sampling Algorithms
Collective Variable Sampling Algorithms
Collective Variable Sampling Algorithms
Methods for Predicting Functional Modes
Integrated Servers for Structure-Based Function Prediction
Integrated Servers for Function Prediction from Structure
The Problem of Function Prediction from Structure
Integrated Servers for Structure-Based Function Prediction
Structure-Function Prediction Methods
Integrated servers for structure-based function prediction
Integrative servers for structure-based function prediction
Integrative Servers for Structure-Based Function Prediction
Integrated Servers for Structure-Based Function Prediction
Integrated servers for structure-based function prediction
Integrative Servers for Function Prediction from Structure
Integrative servers for structure-based function prediction
Structure-based methods employed by ProFunc
Integrated servers for function prediction from structure
Evaluation of structural methods
Integrated Servers for Structure-Based Function Prediction
Examples: prediction of the function of structures obtained in structural genomics projects
Examples of large-scale protein function prediction
Examples: predicting the function of structures obtained from structural genomics projects
Examples: prediction of the function of structures obtained in structural genomics projects
Examples: prediction of the function of structures obtained through structural genomics projects
Examples: prediction of function for structures obtained in structural genomics projects
Prediction of Protein Function Based on Theoretical Models
Protein Models as a Publicly Available Resource
Prediction of protein function based on their theoretical models
Protein models as a publicly available resource
Protein models as a publicly accessible resource
Accuracy and added value of model-based predictions
Predicting Protein Function from Theoretical Models
Accuracy and Added Value of Model-Based Predictions
Prediction of Protein Function Based on Theoretical Models
Practical Application
Plasticity of Catalytic Site Residues
Practical Applications
Protein Function Prediction Based on Theoretical Models
Prediction of Protein Function Based on Theoretical Models
Practical Application
Prediction of Ligand Specificity
Structure Modeling of Alternatively Spliced Isoforms