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Protein Modeling and Structural Prediction

  • Sebastian Kelm
  • Yoonjoo Choi
  • Charlotte M. Deane

Abstract

Proteins perform crucial functions in every living cell. The genetic information in every organismʼs DNA encodes the proteinʼs amino acid sequence, which determines its three-dimensional structure, which, in turn, determines its function. In this postgenomic era, protein sequence information can be obtained relatively easily through experimental means. Sequence databases already contain millions of protein sequences and continue to grow. Structural information, however, is harder to obtain through experimental means – we currently know the structure of about 75000 proteins. Knowledge of a proteinʼs structure is extremely useful in understanding its molecular function and in developing drugs that bind to it. Thus, computational techniques have been developed to bridge the ever-increasing gap between the number of known protein sequences and structures.

In addition to proteins in general, this chapter discusses the specific importance of membrane proteins, which make up about one-third of all known proteins. Membrane proteins control communication and transport into and out of every living cell and are involved in many medically important processes. Over half of current drug targets are membrane proteins.

A brief introduction to protein sequence and structure is followed by an overview of common techniques used in the process of computational protein structure prediction. Emphasis is put on two particularly hard problems, namely protein loop modeling and the structural prediction of membrane proteins.

Keywords

Dihedral Angle Protein Structure Prediction Steric Clash Template Protein Model Quality Assessment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

3-D

three-dimensional

BLAST

basic local alignment search tool

BLOSUM

blocks of amino acids substitution matrix

CASP

critical assessment of techniques for protein structure prediction

DNA

deoxyribonucleic acid

DSSP

define secondary structure of proteins

ESST

environment-specific substitution table

HiAcc

high accuracy

HiCov

high coverage

MQAP

model quality assessment program

PDB

protein data bank

PHAT

predicted hydrophobic and transmembrane

QMEAN

qualitative model energy aNalysis

RMSD

root-mean-square deviation

RNA

ribonucleic acid

SLIM

scorematrx leading intramembrane

TM

transmembrane

log

logistic regression

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Copyright information

© Springer-Verlag 2014

Authors and Affiliations

  1. 1.Department of StatisticsUniversity of OxfordOxfordUK
  2. 2.Department of Computer ScienceDartmouth CollegeHanoverUSA
  3. 3.Department of StatisticsUniversity of OxfordOxfordUK

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