Geometric methods in structural computational biology

OpenStax

@

Structural computational biology: introduction and background

0.1 Proteins and their significance to biology and medicine

0.2 Protein structure

0.3 Experimental methods for protein structure determination

0.4 X-ray crystallography

0.6 Electron diffraction

0.7 Structure prediction of large complexes

0.8 Protein structure repositories

0.9 Visualizing protein structures

0.10 Visualizing hla-aw with vmd

0.11 Visualizing hla-aw with protein explorer

1 Representing proteins in silico and protein forward kinematics

2 Protein inverse kinematics and the loop closure problem

3 Molecular shapes and surfaces

3.1 Introduction

3.2 Representing shape

3.3 Alpha-shapes

3.4 Computing the alpha-shape: delaunay triangulation

3.5 Weighted alpha shapes

3.6 Calculating molecular volume using α-shapes

4 Molecular distance measures

5 Protein classification, local alignment, and motifs

6 Dimensionality reduction methods for molecular motion

6.1 Introduction

6.2 Dimensionality reduction

6.3 Principal components analysis

6.4 Pca of conformational data

6.5 Non-linear methods

6.6 Isometric feature mapping (isomap)

7 Robotic path planning and protein modeling

8 Motion planning for proteins: biophysics and applications

9 Protein-ligand docking, including flexible receptor-flexible ligand

9.1 Background and motivation

9.2 Components of a docking program

9.3 Ligand placement algorithm

9.4 Scoring function

9.5 Explicit force field scoring function

9.6 Empirical scoring functions

9.7 Knowledge-based scoring functions

9.8 Rigid receptor docking

9.9 Parameterization of the problem

9.10 Examples of rigid-receptor docking programs

9.11 Autodock 3.0

9.12 Search technique

9.13 Scoring function

9.15 Search technique

9.16 Scoring function

9.18 Search technique

9.19 Scoring function

9.21 Flexible receptor docking

9.22 Introduction

9.23 Flexibility representations

9.24 Soft receptors

9.25 Selection of specific degrees of freedom

9.26 Multiple receptor structures

9.27 Molecular simulations

9.28 Collective degrees of freedom

Homework assignments

Assignment 1: visualization and ranking of protein conformations

1 Assignment 2: performing rotations

2 Assignment 3: inverse kinematics

Source: OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6

	Fireside Poets Quiz By Alec Moffit Start Quiz
	5 Sociology 05 Socialization MCQ By OpenStax Start Quiz
	3 Understanding Societies MCQ By Jessica Collett Start Quiz
	6 Microbiology Midterm Practice By Madison Christian Start Test
	1 Understanding Societies 1 By Jessica Collett Start Exam
	Fundamentals of electrical engineering i By OpenStax Read Online Course
	11 Neuroanatomy 11 The Cerebellum By Stephen Voron Start Quiz
	46 Biology 46 Ecosystems MCQ By OpenStax Start Quiz
	Statistics Final Review By Madison Christian Start Exam
	American Government MCQ By Saylor Foundation Start Quiz