Computational Resources for Protein Structure prediction


One of the key challenges in protein science is determining three dimensional structure from amino acid sequence. Although experimental methods for determining protein structures are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. Various computational tools have been developed that predict different levels of protein structural hierarchy. List of important tools for the prediction of protein structure is given below.

Servers integrated at CRDD

Server Description
APSSP2This server predicts secondary structure of protein's from their amino acid sequence with high accuracy. It uses the multiple alignment, neural network and MBR techniques. This server participates in number of world wide competition like CASP, CAFASP and EVA (Raghava 2002; CASP5 A-31).
PROCLASSPrediction of structural class of proteins such as Alpha or Beta or Alpha+Beta or Alpha/Beta (Raghava 1999; J. Biosciences 24:176).
PSAThis server allow user to analysis of protein sequence and present the analysis in Graphical and Textual format. This allows property plots of 36 parameter (like Hydrophobicity Plot, Polarity, Charge) of single sequence and multiple sequence alignment (Raghava 2001; Biotech Software and Internet Report, 2:255).
RPFOLDIt allows to predict top 5 similar fold in PDB (Protein DataBank) for a given protein sequence (query).
BTevalBenchmarking of Beta Turn prediction methods on-line via Internet (Kaur and Raghava 2002; Bioinformatics 18:1508-14). The user can see the performance of their method or existing methods (Kaur and Raghava 2003; Journal of Bioinformatics and Computational Biology 1:495-504)
BetatTPred2Prediction of Beta Turns in Proteins using Neural Network and multiple alignment techniques. This is highly accurate method for beta turn prediction (Kaur and Raghava 2003; Protein Science 12:627).
GammaPredPrediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information (Kaur and Raghava 2003; Protein Science; 12:923).
AlphaPredPrediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information (Kaur & Raghava 2004; Proteins 55:83-90).
BetaTPredA server for predicting Beta Turns in proteins using existing statistical methods. This allows consensus prediction from various methods (Kaur and Raghava 2002; Bioinformatics 18:498).
CHpredictThe CHpredict server predict two types of interactions: C-H...O and C-H...PI interactions. For C-H...O interaction, the server predicts the residues whose backbone Calpha atoms are involved in interaction with backbone oxygen atoms and for C-H...PI interactions, it predicts the residues whose backbone Calpha atoms are involved in interaction with PI ring system of side chain aromatic moieties.
AR_NHPredA web server for predicting the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure (Kaur and Raghava 2004; Febs Lett. 564:47-57)
TBBpredIt predicts the whether a protein is outer membrane betat-barrel protein or not. It also predicts transmembrane Beta barrel regions in a given protein sequence. (Natt et al. 2004; Proteins 56:11-8).
BetaturnsThis server predicts the beta turns and their types in a protein from its amino acid sequence (Kaur and Raghava 2004; Bioinformatics 20:2751-8).
PEPstrThe Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that ?-turn is an important and consistent feature of small peptides in addition to regular structures.
BhairPredPrediction of beta hairpins in proteins using ANN and SVM techniques. In this method secondary structure and multiple sequence alignment are used to predict the beta hairpins (Kumar et al. 2005; Nucleic Acids Res. 33:W154-9)
SARpredPrediction of real value of surface accessibility instead of buried or exposed residues in proteins from amino acid sequence (Garg et al. 2005; Proteins)
OXbenchA bench-mark for evaluation of protein multiple sequence alignment accuracy (Raghava et al. 2003; BMC Bioinformatics 4-47).


Webserver/Databases/Mirror Sites

Super Secondary Structure Prediction

Server Description
transFoldsuper-secondary structure prediction of transmembrane beta-barrel proteins


Secondary structure Assignment

Server Description
StrideProtein secondary structure assignment.
PROSSDihedral Angle-Based Secondary Structure Assignment.


Tertiary Structure Prediction

Comparative Modelling

Server Description
ModBaseContains theoretically calculated models, not experimentally determined structures.
GTOPConsisting of data analyses of proteins identified by various genome projects.
ModellerUsed for homology or comparative modeling of protein three-dimensional structures.


Assessing Tertiary Structure

Server Description
MOLPROBITYOffering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes.
PROCHECKChecks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.


Secondary Structure Prediction(sequence based)

Server Description
PSIPREDProtein Structure Prediction Server.
PROFSecondary Structure Prediction System.
PROMOTIF v2.0Provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files.


Transmembrane Helix Prediction

Server Description
MEMSTATProtein Transmembrane Helix Prediction.


Links







Secondary Structure Prediction (Sequence based)
Jpred
NNPREDICT
HNN
JUFO
PORTER
SOPMA
ssPRO
COUDES
PredictProtein
Super secondary Structure Prediction
TurnPred
Secondary Structure Assignment
DSSP
Transmembrane Helix Prediction
HMMTOP
TMHMM
TMpred
THUMBUP
UMDHMM
TUPS
SVMTOP
Protein Structure Database
PDB
SCOP
CATH
PSdb
MMDB
MSD
Tertiary structure Prediction
Comparative Modelling
SWISS-MODEL
3D-JIGSAW
CPHmodels 2.0
ESyPred3D 1.0
SDSC1
GENO 3D
Threading
3D-PSSM
PHYRE
FUFUE
SAM
THREADER
mGENThreader
Ab-initio
ROSETTA
Accessing Tertiary Structure
WHATIF
PROSA
HARMONY
VADAR
WHAT CHECK
Verify 3D
NQ-Flipper