| ViPs-
viral protein structure resource |
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| Three-dimensional structure
of protein provides information pertaining to biological
mechanism, function, interactions, and has significant
implications in designing anti-viral drugs and protein-based
vaccines. |
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| VirGen
- A Comprehensive Viral Genome Resource |
|
| VirGen a comprehensive viral
genome resource, which organizes the 'sequence space'
of viral genomes in a structured fashion. It has been
developed with an objective to serve as an annotated and
curated database for complete viral genome sequences |
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| Spectral
Repeat Finder (SRF) |
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| Spectral Repeat Finder (SRF)
is a program to find repeats through an analysis of the
power spectrum of a given DNA sequence. |
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| GOPAM-
Gene Ontology Based Prediction Analysis of MicroArray
Suite |
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| Gopam is a comprehensive web
based tool for high throughput analysis of microarray
data. GOPAM takes advantage of the GO annotation of genes
to biological terms for performing a fully automated top-down
approach to analyze microarray data. |
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| Pdb
Sequence Search Tool |
|
| Sequence Retrieval, Aminoacid
composition, Molecular Weight and Volume, Sequence Length
Search, Molecular Weight Search, Identical Pattern Matching,
Similar Pattern Matching, Isoelectric Point |
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| Biomolecules
Segment Display Device (BSDD) |
|
| An interactive web-based display
tool, Biomolecules Segment Display Device (BSDD), has
been developed to search for and visualize a user-defined
motif or fragment among the protein structures available
in the Protein Data Bank (PDB). In addition, the tool
works for the structures available in a selected sub-set
of non-homologous protein structures (25% and 90% sequence
identity). |
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| PDB
Goodies |
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| PDB Goodies (version 1.0) is
a web based Graphical User Interface (GUI) to manipulate
the Protein Data Bank (PDB) file containing the three
dimensional atomic coordinates of protein structures. |
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| Ramachandran
Plot (RP) |
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| A World Wide Web graphics package
has been developed to display the main chain torsion angles
phi,psi (Ramachandran angles) in a protein of known structure.
This package allows users to find the Ramachandran angles
for a particular amino acid type, present in the protein
structure |
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| Conformation
Angles Package (CAP) |
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| A graphics package developed
to display all side chain conformation angles of the user
selected residue in a given protein structure. |
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| Water
Analysis Package (WAP) |
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| A web based tool for the analysis
of water molecules in protein structures |
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| Symmetry
Equivalent Molecules (SEM) |
|
| Symmetry Equivalent Molecules,
is a web based Graphical User Interface to generate and
visualize the symmetry equivalent molecules (proteins
and nucleic acids). In addition, the program allows the
users to save the three-dimensional atomic coordinates
of the symmetry equivalent molecules in the local machine. |
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| Fragment
Finder |
|
| FF (Fragment Finder) is a web-based
interactive search engine developed to retrieve the userdesired
similar 3D structural fragments from the selected subset
of 25 or 90% non-homologous protein chains. The search is
based on the comparison of the main chain backbone conformational
angles (fandw). |
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| 3D
Structural Superimposition (3D-SS) |
|
| 3dSS is a web-based interactive
computing server, primarily designed to aid researchers,
to superpose two or several three-dimensional protein
structures. In addition, the server can be effectively
used to find the invariant and common water molecules
present in the superposed homologous protein structures. |
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| Protein
Structure Analysis Package (PSAP) |
|
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| Ramachandran
Plot for Multiple Structures (RPMS) |
|
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|
Consensus Secondary Structure Prediction (CSSP) |
|
| This is created to predict
the consensus secondary structure using well known algorithms
from the literature. Furthermore, the server allows users
to see the occurrence of predicted secondary structural
elements in other structure and sequence databases and
to visualize predicted helices as a helical wheel plot.
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| ChemGenome
|
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| Genome analysis entails the
prediction of genes in uncharacterized genomic sequences.
The objective is to be able to take a newly sequenced
uncharacterized genome and break it up into introns, exons,
repetitive DNA sequences, transposons etc. and other elements. |
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| Bhageerath
|
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| Protein Structure Prediction
Software |
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| Bhageerath
H |
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| A Homology ab-intio Hybrid
Web server for Protein Tertiary Structure Prediction |
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| Sanjeevini
In-Silico Drug Design Software |
|
| Sanjeevini software has been
developed as a computational pathway paving the way expressely
towards automating lead design, making any number of known
or new candidate molecules out of a small but versatile
set of building blocks called templates, screening them
for drug likeness, optimizing their geomtery, determing
partial atomic charges and assigning other force field
parameters, docking the candidates in the active site
of a given biological target , estimating the interaction/bidning
energy, peforming molecular dynamics simulations with
explicit solvent and salt on the biomolecular target,
the candidate and the complex followed by a rigourous
analysis of the binding free energy for further optimization.
Presetly we have coupled Sanjeevini with AMBER and GAMESS
for molecular mechanics and quantam mechanics calculations,
respectively. |
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| ABC
DNA Simulation |
|
| The ABC (Ascona B-DNA Consortium)
initiative was undertaken by an international collaborative
effort involving nine research groups. ABC Simulations
is a computationally intensive project aimed at carrying
out molecular dynamics (MD) simulations including water
and counterions on B-DNA oligomers containing all 136
unique tetranucleotide base sequences.The ABC (Ascona
B-DNA Consortium) initiative was undertaken by an international
collaborative effort involving nine research groups. ABC
Simulations is a computationally intensive project aimed
at carrying out molecular dynamics (MD) simulations including
water and counterions on B-DNA oligomers containing all
136 unique tetranucleotide base sequences. |
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| Lead
Invent A spin off company from SCFBio. |
|
| LeadInvent is a life sciences
R&D Company based out of Biotech Centre, University of
Delhi South Campus. We combine proprietary computational
biology technologies: Computer Aided Drug Discovery (CADD)
algorithms and Protein Structure algorithms with high
performance computing to develop viable therapeutic lead
molecules. |
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