Secondary and Tertiary Structure Prediction of Proteins: A Bioinformatic Approach - Complex System Modelling and Control Through Intelligent Soft Computations - page 532

model of high accuracy. Lastly, scope for further research in order to bridge
existing gaps and for developing better secondary and tertiary structure prediction
algorithms is also highlighted.

Keywords Secondary structure prediction Tertiary structure prediction

Ab initio folding/modeling Threading Homology modeling CASP

Abbreviations

PSS Protein secondary structure

SSE Secondary structure elements

UniProtKB UNIversal PROTein resource KnowledgeBase

TrEMBL Translated European molecular biology laboratory

PDB Protein data bank

NMR Nuclear magnetic resonance

FM Free modelling

TBM Template based modelling

GOR Garnier-Osguthorpe-Robson

NNSSP Nearest-neighbor secondary structure prediction

ANN Arti cial neural networks

SVM Support vector machines

SOV Segment overlap

CASP Critical assessment of protein structure prediction

EVA EValuation of automatic protein structure prediction

FR Fold recognition

BLAST Basic local alignment search tool

PSI-BLAST Position speci c iterative basic local alignment search tool

MEGA Molecular evolutionary genetics analysis

PHYLIP PHYLogeny inference package

GROMACS GROningen machine for chemical simulations

AMBER nement

CHARMM Chemistry at HARvard molecular mechanics
GDT Global displacement test
PROCHECK PROtein structure CHECK
PROSA

Assisted model building and energy re

PROtein structure analysis

MAT MonoAmine transporters

HMM Hidden Markov model

CPU Central processing unit

RPS-BLAST Reversed position speci c BLAST