Protein Structure Analysis Tools
 
 
SUPER IMPOSE   Biomolecules Segment Display Device (BSDD)   Ramachandran Plot (RP)   Conformation Angles Package (CAP)
     

Fits two molecules and calculates the RMSD between them.

Developed and maintained by Supercomputing Facility For Bioinformatics and Computational Biology, IIT Delhi

 

For searching and visualizing user-defined motif or fragment among the protein structures available in the Protein Data Bank (PDB)

Developed and maintained by Indian Institute of Science, Banglore

 

Allows users to find the Ramachandran angles for a particular amino acid type, present in the protein structure

Developed and maintained by Indian Institute of Science, Banglore

 

A graphics package developed to display all side chain conformation angles of the user selected residue in a given protein structure

Developed and maintained by Indian Institute of Science, Banglore

Water Analysis Package (WAP)   Symmetry Equivalent Molecules (SEM)   CADB - 3.0   SSEP - 2.0
     

A web based tool for the analysis of water molecules in protein structures.

Developed and maintained by Indian Institute of Science, Banglore

 

A web based Graphical User Interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids).

Developed and maintained by Indian Institute of Science, Bangalore

 

A standalone GUI tool to identify and analyze non templated nucleotide additions and trimming.

Developed and maintained by International Centre for Genetic Engineering and Biotechnology

 

Secondary structural elements of proteins - protein structure analysis

Developed and maintained by IISc, Bangalore

3dSS   PROTein FRACTals   ContPlot   ConfPlot
     

3dSS is a web based interactive computing server, primarily designed to aid researchers, to superpose two or several three dimensional protein structures

Developed and maintained by Indian Institute of Science, Bangalore

 

PROTein FRACTals: A server to analyse protein interior and protein exterior properties with fractal dimension

Developed and maintained by University of Pune.

 

Identification of residues deviating from the average values of accessible surfac

Developed and maintained by Bose Institute,Kolkata

 

Display of conformational features of main- and side- chains.

Developed and maintained by Bose Institute,Kolkata

IntGeom1   IntGeom2   RM2TS   BHAGEERATH-H
     

Interaction geometry for planar side chains

Developed and maintained by Bose Institute,Kolkata

 

Sulfur-aromatic interaction geometry

Developed and maintained by Bose Institute,Kolkata

 

RM2TS: From Ramachandran Maps to Tertiary structures of proteins.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

BHAGEERATH-H: A Homology ab-intio Hybrid Web server for Protein Tertiary Structure Prediction

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

BHAGEERATH   StrGen   C A S S P   Bhageerath-H Strgen
     

BHAGEERATH : An energy based protein structure prediction server

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

Structure generation from given dihedrals.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

Comparative analysis of secondary structure of proteins

Developed and maintained by Birla Institute of Scientific Research

 

Bhageerath-H Strgen is a homology/ab initio hybrid algorithm for protein conformational sampling.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

Radius of Gyration   Hydrophobicity   Packing Fraction   ProRegIn
     

Filters for globular protein evaluation - Radius of Gyration

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

Filters for globular protein evaluation - Hydrophobicity Ratio

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

To evaluate the value of packing fraction for a given protein and to find out whether the value is in acceptable limits for globular protein or not.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

To separate improbable structures from native-like probable structures.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

Protein structure optimizer   ProSEE   Protein Angle Descriptor   ProTSAV
     

The protein structure optimizer minimizes the energy of the protein structure using a combination of steepest descent and conjugate gradient minimization algorithms.

Developed and maintained by Supercomputing Facility for Bioinformatics and Computational Biology, IIT, Delhi

 

Scoring function for protein structure evaluation calculates intramolecular energy of a protein in component-wise break up.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

 

Calculates the angles & dihedral in the main chain of the protein

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhiy

 

ProTSAV is a meta-server, which has a collection of model quality assessment programs that evaluate the quality of a protein and correctness of the structural model.

Developed and maintained by Supercomputing facility for Bioinformatics and computational biology, IIT, Delhi

Persistence Length   Fragment Finder   3d-SS   PSAP
     

A biophysical filter, which calculates the maximum length of the polypeptide chain in one direction.

Developed and maintained by ISupercomputing Facility For Bioinformatics and Computational Biology, IIT Delhi.

 

FF(2.0) is a web-based interactive engine developed to retrieve the user desired similar three-dimensional strutural fragment from the selected subset of 25% or 90% non homologous protein chains.

Developed and maintained by Indian Institute of Science, Banglore.

 

3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several three-dimensional protein structures..

Developed and maintained by Indian Institute of Science, Banglore.

 

Protien structure analysis package is a A web based suite for protein structure analysis.

Developed and maintained by Indian Institute of Science, Banglore.

RamaChandranPlot   BRM-Parser   ALPHAPRED   Ar_NHPred
     

Ramachandran Plot for multiple structures is a web based tool for studying the structural stability of a protein.

Developed and maintained by Indian Institute of Science, Banglore.

 

BLAST and RepeatMasker Parser (BRM-Parser) is a service that provides users a unified platform for easy analysis of relatively large outputs of BLAST (Basic Local Alignment Search Tool) and RepeatMasker programs.

Developed and maintained by CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY, HYDERABAD (BIC @ CCMB).

 

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

The Ar_NHPred server predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

BetaTPred   BetaTPred2   BetaTurns   BhairPred
     

A webserver for predicting -turns in a protein from the amino acid sequence. It allows the user to predict turns in a protein using existing statistical algorithms, to predict the type of -turn and to predict the consensus -turn in a protein.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

A webserver for Prediction of -turns in proteins using neural networks and multiple alignment.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

The aim of Betaturns server is to predict different types of turns such as Types I, II, IV, VIII and non-specific in a given amino acid sequence.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

A webserver for Prediction of beta hairpins in proteins using ANN and SVM techniques.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

RPFOLD   SARpred   TBBpred   HSLpred
     

A fold recognition server for searching protein fold in PDB. It is based on seaquence similarity search and secondary structure alignment technique.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

SARpred, a neural network based method predicts the real value of surface acessibility (SA) by using multiple sequence alignment.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

Transmembrane Beta Barrel prediction server predicts the transmembrane Beta barrel regions in a given protein sequence.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

Hslpred is aN SVM-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins .

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

LGEpred   COPid   ESLPred2   AHTpdb
     

This server allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between amino acid residue and gene expression level.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

a webserver for Composition based identification and classification of proteins.

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

An SVM based methods for predicting the subcellular localization of the eukaryotic proteins using various features of proteins .

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

 

A webserver for Collection and compilation of antihypertensive peptides .

Developed and maintained by INSTITUTE OF MICROBIAL TECHNOLOGY, CHANDIGARH.

             
 
     
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