| Protein
Information Resource (P I R) |
|
| The Universal Protein Resource
(UniProt) provides the scientific community with a single,
centralized, authoritative resource for protein sequences
and functional information. |
| |
|
| National
Center for Biotechnology Information (NCBR) |
|
| The National Center for Biotechnology
Information advances science and health by providing access
to biomedical and genomic information. |
| |
|
| ExPASy |
|
| TSIB Bioinformatics Resource
Portal which provides access to scientific databases and
software tools in different areas of life sciences including
proteomics, genomics, phylogeny, systems biology, population
genetics, transcriptomics etc. |
| |
|
| EMBL
- European Bioinformatics Institute(EBI) |
|
| EMBL-EBI is a centre for research
and services in bioinformatics. It has diversified to
provide data resources in all the major molecular domains
and expanded to include a broad research base. It provides
user support and offers advanced training in bioinformatics. |
| |
|
| Protein
Data Bank (P D B) |
|
| The PDB archive contains information
about experimentally-determined structures of proteins,
nucleic acids, and complex assemblies. |
| |
|
| Protein
Data Bank Japan(P D B j) |
|
| PDBj maintains the database
for the protein structures collaborating with RCSB, PDBe
and BMRB |
| |
|
| Protein
Data Bank Europe(P D B e) |
|
| A European resource for PDB
protein structure deposition and PDB structure annotation
to the wwPDB. |
| |
|
| BMRB
- Biological Magnetic Resonance Bank |
|
| Database for NMR spectroscopy
information on biomolecules. |
| |
|
| GMOD
- Generic Model Organism Database |
|
| Collection of open source software
tools for creating and managing genome-scale biological
databases. |
| |
|
| UniProt |
|
| The mission of UniProt is to
provide the scientific community with a comprehensive,
high-quality and freely accessible resource of protein
sequence and functional information. |
| |
|
| ProtoMap |
|
| An automatic heirarchichal
classification of all SWISSPROT and TrEMBL proteins. |
| |
|
| ICGEB
- International Centre for Genetic Engineering and Biotechnology
|
|
| An International centre for
genetic engineering and Biotechnology. With special regard
to the needs of the developing world. |
| |
|
| TIGRFAMs |
|
| TIGRFAMs is a resource consisting
of curated multiple sequence alignments, Hidden Markov
Models (HMMs) for protein sequence classification, and
associated information designed to support automated annotation
of (mostly prokaryotic) proteins. |
| |
|
| OWL |
|
| A non-redundant composite of
4 publicly-available primary sources: SWISSPROT, PIR (1-3),
GenBank (translation) and NRL-3D. |
| |
|
| CATH |
|
| CATH is a manually curated
classification of protein domain structures. |
| |
|
| SCOP
- Structural Classification of Proteins |
|
| Detailed and comprehensive
description of the structural and evolutionary relationships
between all proteins whose structure is known. As such,
it provides a broad survey of all known protein folds,
detailed information about the close relatives of any
particular protein, and a framework for future research
and classification. |
| |
|
| COG |
|
| Clusters of Orthologous Groups
of proteins (COGs) were delineated by comparing protein
sequences encoded in complete genomes, representing major
phylogenetic lineages. Each COG consists of individual
proteins or groups of paralogs from at least 3 lineages
and thus corresponds to an ancient conserved domain. |
| |
|
| PRINTS |
|
| PRINTS is a compendium of protein
fingerprints. A fingerprint is a group of conserved motifs
used to characterize a protein family |
| |
|
| PROSITE |
|
| First secondary database of
proteins and motifs are encoded as regular expressions,
often simply referred to as patterns. |
| |
|
| BLOCKS |
|
| Multiple-motif database, based
on protein families contained in PROSITE database. |
| |
|
| Pfam
- Protein Family |
|
| A database of protein families
that includes their annotations and multiple sequence
alignments generated using hidden Markov models. |
| |
|
| PDBsum |
|
| A database of protein families
that includes their annotations and multiple sequence
alignments generated using hidden Markov models. |
| |
|
| ProDom
- Protein domain |
|
| ProDom is a comprehensive set
of protein domain families automatically generated from
the UniProt Knowledge Database |
| |
|
| SUPERFAMILY |
|
| SUPERFAMILY is a database of
structural and functional annotation for all proteins and genomes. |
| |
|
| PIRSF
- Protein Information Resource Super Family |
|
| The PIRSF concept is being
used as a guiding principle to provide comprehensive and
non-overlapping clustering of UniProtKB sequences into
a hierarchical order to reflect their evolutionary relationships. |
| |
|
TOOLS
|
|
| CYBIONIX |
|
| Global bioinformatic directory |
| |
|
| ReNaBI
- Reseau National des plates-formes Bioinformatiques |
|
| A bioinformatics network built
upon the many platforms of the different institutes. Altogether,
these platforms constitute a major resource for the scientific
community: expertise, knowledge, know-how, computing power,
etc. |
| |
|
| Protein/Aminoacid
databases |
|
| The links available into some
sort of system to allow an investigator to quickly find
an appropriate database without having to read through
a mass of links. |
| |
|
PATHWAY DATABASE
|
|
| KEGG
- Kyoto Encyclopedia of Genes and Genomes |
|
| A bioinformatics resource for
linking genomes to life and the environment. This database
is a collection of online databases, dealing with genomes,
enzymatic pathways and biological chemicals. |
| |
|
| PANTHER
- Protein ANalysis THrough Evolutionary Relationships |
|
| A database of protein families
that includes their annotations and multiple sequence
alignments generated using hidden Markov models. |
| |
|
| BioCyc |
|
| BioCyc is a collection of 1690
Pathway/Genome Databases. Each database in the BioCyc
collection describes the genome and metabolic pathways
of a single organism. |
| |
|
| MetaCyc |
|
| MetaCyc is a database of nonredundant,
experimentally elucidated metabolic pathways. |
| |
|
| INOH
- Integrating Network Objects with Hierarchies |
|
| Metabolic pathway database. |
| |
|
| PathCase
- Pathways Database System |
|
| Each PathCase application contains
a different set of tools. All applications store, query,
and visualize metabolic pathways, in addition to their
specialized tasks. |
| |
|
| SMPDB
- The Small Molecule Pathway Database |
|
| Small Molecule Pathway Database
is an interactive, visual database containing more than
350 small molecule pathways found in humans. |
| |
|
| MMMDB
- Mouse Multiple Tissue Metabolome Database |
|
| Provides comprehensive and
quantitative metabolomic information for multiple tissues
from single mice. |
| |
|
| EcoCyc |
|
| EcoCyc is a scientific database
for the bacterium Escherichia coli K-12 MG1655. The EcoCyc
project performs literature-based curation of the entire
genome, and of transcriptional regulation, transporters,
and metabolic pathways. |
| |
|
VARIANTS
|
|
| Variome.net |
|
| An openfree web resource and
encyclopedia of world wide SNP (Single Nucleotide Polymorphism)
researchers and supports the international genome variance
researches by collecting, organizing, analyzing, and disseminating
variome information. |
| |
|
| HapMap
- Haplotype Map |
|
| Public resource that will help
researchers find genes associated with human disease and
response to pharmaceuticals. |
| |
|
GENOME
|
|
| DDBJ
- DNA Data Bank of Japan |
|
| DNA Data Bank of Japan is the
sole nucleotide sequence data bank in Asia, which is officially
certified to collect nucleotide sequences from researchers
and to issue the internationally recognized accession
number to data submitters. |
| |
|
| The
Gene Ontology |
|
| Standardizing the representation
of gene and gene product attributes across species and
databases. |
| |
|
| TRRD
- Transcription Regulatory Region Database |
|
| TRRD is a unique information
resource, accumulating information on structural and functional
organization of transcription regulatory regions of eukaryotic
genes. Only experimentally confirmed information is included
into TRRD. |
| |
|
| The
Eukaryotic Promoter Database |
|
| An annotated non-redundant
collection of eukaryotic POL II promoters, for which the
transcription start site has been determined experimentally. |
| |
|
| ChipDB |
|
| It allows the user to search
through the collection of strains, experiments, and genetic
features (read: genes) in the database. |
| |
|
| GUS |
|
| An extensive relational database
schema and associated application framework designed to
store, integrate, analyze and present functional genomics
data. |
| |
|
| GeneCards |
|
| GeneCards is a searchable,
integrated, database of human genes that provides concise
genomic related information, on all known and predicted
human genes. |
| |
|
| Sanger
Institute |
|
| A leader genome research institute
in the Human Genome Project, now focused on understanding
the role of genetics in health and disease |
| |
|
| ENSEMBL |
|
| The Ensembl project produces
genome databases for vertebrates and other eukaryotic
species, and makes this information freely available online. |
| |
|
| ACeDB |
|
| AceDB is a database designed
specifically for handling genome and bioinformatic data.AceDB
was originally developed for the C.elegans genome project.
However, the tools in it have been generalized to be much
more flexible and the same software is now used for many
different genomic databases from bacteria to fungi to
plants to man. It is also increasingly used for databases
with non-biological content. |
| |
|
| ASRP |
|
| A searchable database of published
miRNA sequences and annotation. Each entry in the miRBase
Sequence database represents a predicted hairpin portion
of a miRNA transcript (termed mir in the database), with
information on the location and sequence of the mature
miRNA sequence (termed miR). Both hairpin and mature sequences
are available for searching and browsing, and entries
can also be retrieved by name, keyword, references and
annotation. |
| |
|
| MaizeSequenceDatabase |
|
| This browser provides the latest
sequence and annotation of the Zea mays ssp. mays genome
resulting from the Maize Genome Sequencing Project. The
browser is based on the AGI Agarose FPC Map and on BAC
clone sequences contained therein. Sequencing of the B73
cultivar commenced in November 2005 as part of a 3-year
multi-institutional collaboration funded jointly by the
NSF, USDA and DOE. The strategy is to individually sequence
a set BAC clones across a minimal-tiling path. Gene space
will be identified and sequenced to finished quality.
As of February 27, 2008, the consortium completed the
draft sequence of the maize genome and will improve the
sequence through the end of 2008. |
| |
|
| HIV
Sequence database |
|
| The HIV databases contain data
on HIV genetic sequences, immunological epitopes, drug
resistance-associated mutations, and vaccine trials. |
| |
|
| RDP
- Ribosomal DataBase Project |
|
| The Ribosomal Database Project
(RDP) provides ribosome related data and services to the
scientific community, including online data analysis and
aligned and annotated Bacterial and Archaeal small-subunit
16S rRNA sequences. |
| |
|
| SiRNA
databases and resources for RNA interference studies |
|
| The discovery of reagents to
inhibit RNA synthesis and translation has revolutionized
the study of biological processes. These tools include
small inhibitory RNA (siRNA), small hairpin RNA (shRNA)
and ribozymes. |
| |
|
| GRAMENE |
|
| Gramene is a curated, open-source,
data resource for comparative genome analysis in the grasses.
Our goal is to facilitate the study of cross-species homology
relationships using information derived from public projects
involved in genomic and EST sequencing, protein structure
and function analysis, genetic and physical mapping, interpretation
of biochemical pathways, gene and QTL localization and
descriptions of phenotypic characters and mutations. |
| |
|
| Allen
Institute of Brain science |
|
| A growing collection of online
public resources integrating extensive gene expression
and neuroanatomical data, complete with a novel suite
of search and viewing tools. |
| |
|
| SGD
- Saccharomyces Genome Database |
|
| A scientific database of the
molecular biology and genetics of the yeast Saccharomyces
cerevisiae. |
| |
|
| PomBase
- Pombe Database |
|
| PomBase is a comprehensive
database for the fission yeast Schizosaccharomyces pombe,
providing structural and functional annotation, literature
curation and access to large-scale data sets. |
| |
|
| S.
Pombe :GeneDB - Schizosaccharomyces pombe: Gene DataBase |
|
| This database contains all
S. pombe (fission yeast) known and predicted protein coding
genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs,
snoRNAs and other known and predicted non-coding RNAs. |
| |
|
| 1001
genomes |
|
| The 1001 Genomes Project, launched
at the beginning of 2008, has as a goal to discover the
whole-genome sequence variation in 1001 strains (accessions)
of the reference plant Arabidopsis thaliana. The resulting
information is paving the way for a new era of genetics
that identifies alleles underpinning phenotypic diversity
across the entire genome and the entire species. |
| |
|
| TAIR
- The Arabidopsis Information Resource |
|
| Maintains a database of genetic
and molecular biology data for the model higher plant
Arabidopsis thaliana |
| |
|
| MaizeGDB
- Maize Genome DataBase |
|
| MaizeGDB is a community-oriented,
long-term, federally funded informatics service to researchers
focused on the crop plant and model organism Zea mays. |
| |
|
| FlyBase |
|
| New and more biologically meaningful
organization of the genomic data presented on GBrowse
for D. melanogaster. |
| |
|
| WormBase |
|
| WormBase at Caltech (at Pasadena,
CA, USA) currently has seven full-time biological curators
as well as several bioinformaticians and software developers.
The Caltech group annotates gene expression patterns,
gene regulation, functional descriptions, phenotypes,
microarray data, cell functions, and protein and gene
interactions. We continually try to obtain, store and
display whatever information has become most relevant
to our community. |
| |
|
| ZFIN
- The Zebrafish Information Network |
|
| Zebra fish organism model
database. |
| |
|
| MGI
- Mouse Genome Informatics |
|
| MGI is the international database
resource for the laboratory mouse, providing integrated
genetic, genomic, and biological data to facilitate the
study of human health and disease |
| |
|
| RGD
- Rat Genome Database |
|
| Excellent source of information
about rat strains and their associated physiology, phenotypes
and diseases. |
| |
|
| SCOR
- Structural Classification of RNA |
|
| Designed to provide a comprehensive
perspective and understanding of RNA motif structure,
function, tertiary interactions and their relationships. |
| |
|
| Noncoding
RNA database |
|
| The noncoding RNA (ncRNA) database
is intended to provide information on the sequences and
functions of transcripts which do not code for proteins,
but perform regulatory roles in the cell. Currently, the
database includes over 30,000 individual sequences from
99 species of Bacteria, Archaea and Eukaryota. |
| |
|
|
miRBase - Micro RNA sequences dataBase |
|
| Database of published miRNA
sequences and annotation. |
| |
|
| TissueInfo
|
|
| TissueInfo is a program that
determines the tissue expression profile of a sequence. |
| |
|
| Nucleic
acid database |
|
| A repository of three-dimensional
structural information about nucleic acids. |
| |
|
DRUG DATABASES
|
|
| DrugBank
|
|
| The DrugBank database is a
unique bioinformatics and cheminformatics resource that
combines detailed drug (i.e. chemical, pharmacological
and pharmaceutical) data with comprehensive drug target
(i.e. sequence, structure, and pathway) information. The
database contains 6707 drug entries including 1436 FDA-approved
small molecule drugs, 134 FDA-approved biotech (protein/peptide)
drugs, 83 nutraceuticals and 5086 experimental drugs.
Additionally, 4228 non-redundant protein (i.e. drug target/enzyme/transporter/carrier)
sequences are linked to these drug entries. Each DrugCard
entry contains more than 150 data fields with half of
the information being devoted to drug/chemical data and
the other half devoted to drug target or protein data. |
| |
|
| Therapeutic
Target Database |
|
| A database to provide information
about the known and explored therapeutic protein and nucleic
acid targets, the targeted disease, pathway information
and the corresponding drugs directed at each of these
targets. Also included in this database are links to relevant
databases containing information about target function,
sequence, 3D structure, ligand binding properties, enzyme
nomenclature and drug structure, therapeutic class, clinical
development status. |
| |
|
| PharmGKB
- The Pharmacogenomics Knowledge Base |
|
| Pharmacogenomic knowledge database.
An extensive web resource for analyzing 332828 drug-target
interactions. |
| |
|
TOOLS AND NUCLEIC ACID
|
|
| ExPASy
|
|
| SIB Bioinformatics Resource
Portal which provides access to scientific databases and
software tools in different areas of life sciences including
proteomics, genomics, phylogeny, systems biology, population
genetics, transcriptomics etc. |
| |
|
| NCBI
- National Centre for Biotechnology Information |
|
| Provide tools to analyze biological
data using NCBI software |
| |
|
| |
|
| EMBL-EBI
- European Molecular Biology Laboratory-European Bioinformatics
Institute |
|
| EMBL-EBI is a centre for research
and services in bioinformatics. It has diversified to
provide data resources in all the major molecular domains
and expanded to include a broad research base. It provides
user support and offers advanced training in bioinformatics. |
| |
|
| GLIMMER/
GlimmerHMM -
Gene Locator and Interpolated Markov
ModelER/ Gene Locator and Interpolated Markov ModelER
Hidden Markov Model |
|
| Glimmer is a system for finding
genes in microbial DNA, especially the genomes of bacteria,
archaea, and viruses. Glimmer (Gene Locator and Interpolated
Markov ModelER) uses interpolated Markov models (IMMs)
to identify the coding regions and distinguish them from
noncoding DNA. |
| |
|
| GeneZilla
|
|
| GeneZilla is a state-of-the-art
gene finder based on the Generalized Hidden Markov Model
framework, similar to Genscan and Genie. It is highly
reconfigurable and includes software for retraining by
the end-user. It is written in highly optimized C++. The
run time and memory requirements are linear in the sequence
length, and are in general much better than those of competing
systems, due to GeneZilla's novel decoding algorithm.
Graph-theoretic representations of the high scoring open
reading frames are provided, allowing for exploration
of sub-optimal gene models. It utilizes Interpolated Markov
Models (IMMs), Maximal Dependence Decomposition (MDD),
and includes states for signal peptides, branch points,
TATA boxes, CAP sites, and will soon model CpG islands
as well. |
| |
|
| GENESCAN
|
|
| Identification of complete
gene structures of a genomic DNA. |
| |
|
| Gene
Finder |
|
| To find splice sites and protein
coding exons, construct gene model and recognize the promotor
and poly-A region. |
| |
|
| ORFFinder
- Open Readomg Frame Finder |
|
| This web page is designed to
align a mRNA sequence to a genomic sequence to find
the exons in a gene. The two sequence must be from the
same species and so highly homolgous for the common regions.
If an open reading frame is selected that too is included
in the alignment. |
| |
|
| BioGPS
|
|
| A free extensible and customizable
gene annotation portal, a complete resource for learning
about gene and protein function. |
| |
|
| ATTED
|
|
| It provides co-regulates gene
relations to estimate gene function. |
| |
|
| AnDom
|
|
| This WEB tool helps to assign
structural domains to protein sequences and to classify
them according to SCOP. |
| |
|
| DIURNAL |
|
| DIURNAL is a web tool that
allows you to search and visualize diurnal and circadian
gene expression profiles for your favorite Arabidopsis
genes. |
| |
|
| SBASE
|
|
| Domain prediction tool. |
| |
|
| DSSP
- Database of Secondary Structure Assignments |
|
| The DSSP program was designed
by Wolfgang Kabsch and Chris Sander to standardize secondary
structure assignment. DSSP is a database of secondary
structure assignments (and much more) for all protein
entries in the Protein Data Bank (PDB). |
| |
|
| Target
Optimisation Utility |
|
| TarO analyses a protein sequence
by a large number of bioinformatics techniques. These
include crystallisation propensity prediction, orthologue
searching, and many other sequence based calculations. |
| |
|
| Mobyle
|
|
| A framework and web portal
specifically aimed at the integration of bioinformatics
software and databanks. |
| |
|
| PredictProtein
|
|
| PredictProtein integrates feature
prediction for secondary structure, solvent accessibility,
transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions,
intra-residue contacts, protein-protein and protein-DNA
binding sites, sub-cellular localization, domain boundaries,
beta-barrels, cysteine bonds, metal binding sites and
disulphide bridges. |
| |
|
| PSCA
- Protein Sequence Comparative Analysis |
|
| Protein Sequence Comparative
Analysis (PSCA) is an integrated web tool for comparative
analysis of protein sequence. It analyzes protein sequence
in multiple layers as domains and families, secondary
structure feature, similarity of PDB protein structures,
protein structure prediction and protein homologue. The
PSCA user interface is supported by the server and database
of Joint Center for Structural Genomics (JCSG). |
| |
|
| FunClust |
|
| FunClust is a web server for
the identification of local functional motifs in a set
of non homologous protein structures. |
| |
|
| The
LabelHash server |
|
| The LabelHash suite of programs
and scripts can be used to match point-based structural
motifs to a set of target proteins. |
| |
|
| SABLE
- Solvent AccessiBiLitiEs |
|
| SABLE server can be used for
prediction of the protein secondary structure, relative
solvent accessibility and trans-membrane domains. |
| |
|
| DISULPHIND
|
|
| DISULFIND is a server for predicting
the disulfide bonding state of cysteines and their disulfide
connectivity starting from sequence alone. |
| |
|
| DiANNA
|
|
| DiANNA is a recent state-of-the-art
artificial neural network and web server, which determines
the cysteine oxidation state and disulfide connectivity
of a protein, given only its amino acid sequence. |
| |
|
| Disulfide
by Design |
|
| Disulfide by Design is an application
for the rational design of disulfide bonds in proteins. |
| |
|
| CYSREDOX
- REDOX state of CYSteins |
|
| Predicting redox state of cysteins
in proteins from multiple sequence alignment. |
| |
|
| DSDBASE
- DiSulphide DataBASE |
|
| DSDBASE is a database on disulphide
bonds in proteins that provides information on native
disulphides and those which are stereochemically possible
between pairs of residues in a protein. |
| |
|
| zPicture
|
|
| A dynamic alignment and visualization
tool that is based on blastz alignment program utilized
by PipMaker. |
| |
|
| Bioinformatics
Toolkit |
|
| Collection of tertiary structure
prediction tools. |
| |
|
| PROTEUS |
|
| A web server designed to support
comprehensive protein structure prediction and structure
based annotation. |
| |
|
| SWISSMODEL
|
|
| Fully automated protein structure
homology-modeling server. |
| |
|
| ESyPred3D-
Expert System for the Prediction of proteins 3D structures
|
|
| ESyPred3D is a new automated
homology modeling program. |
| |
|
| 3D-JIGSAW
|
|
| This server builds three-dimensional
models for proteins based on homologues of known structure. |
| |
|
| CASP
- the Critical Assessment of protein Structure Prediction
|
|
| The Critical Assessment of
protein Structure Prediction (CASP) experiments aim at
establishing the current state of the art in protein structure
prediction, identifying what progress has been made, and
highlighting where future effort may be most productively
focused. |
| |
|
| CPHmodels
|
|
| CPHmodels 3.0 is a protein
homology modeling server. The template recognition is
based on profile-profile alignment guided by secondary
structure and exposure predictions. |
| |
|
| 3D-PSSM
|
|
| Combines sequence and structural
information for predicting the structure and/or function
of protein sequence. |
| |
|
| LOOPP@BioHPC
|
|
| LOOPP is a fold recognition
program based on the collection of numerous signals, merging
them into a single score, and generating atomic coordinates
based on an alignment into a homologue template structure. |
| |
|
| STRUCTURE |
|
| |
|
| DALI
server |
|
| The Dali server is a network
service for comparing protein structures in 3D. |
| |
|
| RASMOT-3D
PRO |
|
| RASMOT-3D PRO searches in protein
structure files for proteins possessing a group of residues
in a topology similar to that adopted by a 3D motif given
in input. |
| |
|
| 3dLOGO |
|
| 3dLOGO is a web server that
allows the identification of 3D locally conserved residues
in a set of protein structures. 3dLOGO performs a structural
superimposition of the input structures and identifies
amino acids that are conserved among the different structures.
Such structurally conserved residues are subsequently
used to build a sequence consensus for sequence database
searches. |
| |
|
| STRUCTURE AND FUNCTION |
|
| |
|
| ProFunc
|
|
| A server had been developed
to help identify the likely biochemical function of a
protein from its three-dimensional structure. |
| |
|
| FATCAT
|
|
| FATCAT (Flexible structure
AlignmenT by Chaining Aligned fragment pairs allowing
Twists) is an approach for flexible protein structure
comparison. |
| |
|
| WHAT
IF |
|
| A versatile molecular modelling
package that is specialized on working with proteins and
the molecules in their environment like water, ligands,
nucleic acids, etc. |
| |
|
| I-TASSER
|
|
| I-TASSER server is an Internet
service for protein structure and function predictions. |
| |
|
| ProtSkin
|
|
| Protein sequence conservation
can be a valuable tool to assess functional regions of
a protein. |
| |
|
| SURF's_UP
|
|
| Analysis of functional relationships
in protein families as inferred from protein surface maps
comparison. |
| |
|
| eF-surf
|
|
| Molecular surface of proteins
with the electrostatic potential is a representation of
protein three dimensional structures, which often gives
some clues to infer the function of proteins. |
| |
|
| ProSMoS
|
|
| Programs that assess structural
similarity compare two structures to each other and define
common regions. |
| |
|
| SiteEngine |
|
| Recognizes regions on the surface
of one protein that resemble a specific binding site of
another. |
| |
|
| firestar
|
|
| Predicts functionally important
residues. Predictions are made by evaluating internally
generated alignments using SQUARE. |
| |
|
| LIGAND BINDING SITE |
|
| |
|
| CASTp
|
|
| The tool is meant for binding
sites and active sites of proteins and DNAs are often
associated with structural pockets and cavities. |
| |
|
| 3DLigandSite
|
|
| Prediction of ligand binding
site. |
| |
|
| PocketPicker
|
|
| Identification and evaluation
of surface binding-pockets and occluded cavities are initial
steps in protein structure-based drug design. |
| |
|
| FINDSITE
|
|
| FINDSITE is a threading-based
binding site prediction/protein functional inference/ligand
screening algorithm that detects common ligand binding
sites in a set of evolutionarily related proteins. Crystal
structures as well as protein models can be used as the
target structures. |
| |
|
| IBIS
|
|
| For a given protein sequence
or structure query, IBIS reports physical interactions
observed in experimentally-determined structures for this
protein. IBIS also infers/predicts interacting partners
and binding sites by homology, by inspecting the protein
complexes formed by close homologs of a given query. To
ensure biological relevance of inferred binding sites,
the IBIS algorithm clusters binding sites formed by homologs
based on binding site sequence and structure conservation. |
| |
|
| 3D-SURFER
|
|
| 3D-SURFER is web-based software
for protein surface comparison and analysis. The server
integrates various repertoire of methods to assist in
high throughput screening and visualization of protein
surface comparisons. It takes less than a second to perform
an exhaustive comparison between a single protein surface
to all protein structures in the current PDB. |
| |
|
| MolAxis |
|
| Accurate identification of
channels in macromolecules. |
| |
|
| PESDserver
|
|
| Ligand coordinates are used
to demarcate the binding site. |
| |
|
| ConSurf
Server |
|
| The server for the Identification
of Functional Regions in Proteins. |
| |
|
| METAL BINDING SITES PREDICTION |
|
| |
|
| MetalDetector
|
|
| MetalDetector predicts metal
binding sites in proteins using sequence information alone.
Prediction is limited to transition metals (with the addition
of heme and Fe/S clusters) and to CYS and HIS as ligands.
In this release, MetalDetector predicts the number of
bound metal ions and, for each ion, CYS and HIS ligands
in the sequence. |
| |
|
| GENMR
|
|
| A web server for generating
3D protein structures using NOE-derived distance restraints
and NMR chemical shifts. |
| |
|
| Catalytic
Site Atlas |
|
| Documenting enzyme active sites
and catalytic residues in enzymes of 3D structure. |
| |
|
| DOMAIN |
|
| |
|
| Protein
Peeling v2 |
|
| An approach for splitting a
3D protein structure into proteins units. |
| |
|
| DOMpro
|
|
| Prediction of domains. |
| |
|
| DIAL
|
|
| DIAL is a web server for the
automatic identification of structural domains given the
three-dimensional coordinates of a protein. |
| |
|
| GLOBPLOT
2 |
|
| Intrinsic protein disorder,
domain and globularity prediction. |
| |
|
| PURE
|
|
| PURE is a bioinformatics protocol
to identify putative domains in the Unassigned Regions[UR].
PURE is now available as a web server. Users can submit
the sequence of unassigned regions or linker regions to
predict domains encoded in them. |
| |
|
| Domain
3D |
|
| Domain 3D is a method developed
by Willie Taylor to identify globular domains in protein
structure. |
| |
|
| TLS
Motion Determination |
|
| TLS Motion Determination (TLSMD)
analyzes a macromolecular crystal structure for evidence
of flexibility, e.g. local or inter-domain motions. It
does this by partitioning individual chains into multiple
segments that are modeled as rigid bodies undergoing TLS
(Translation/Libration/Screw) vibrational motion. It generates
all possible partitions up to a maximum number of segments. |
| |
|
| CAVER
|
|
| CAVER is a software tool for
analysis and visualisation of tunnels and channels in
protein structures. Tunnels are void pathways leading
from a cavity buried in a protein core to the surrounding
solvent. Unlike tunnels, channels lead through the protein
structure and their both endings are opened to the surrounding
solvent. Studying of these pathways is highly important
for drug design and molecular enzymology. |
| |
|
| HotPatch
Web Gateway |
|
| HotPatch finds unusual patches
on the surface of proteins, and computes just how unusual
they are (patch rareness), and how likely each patch is
to be of functional importance (functional confidence
(FC).) The statistical analysis is done by comparing your
protein's surface against the surfaces of a large set
of proteins whose functional sites are known. |
| |
|
| MolLoc
|
|
| MolLoc is a web server for the
comparison of molecular surfaces such as binding sites,
cavities and any residue selection. |
| |
|
| PLATINUM |
|
| PLATINUM is designed for calculation
of hydrophobic properties of molecules and their match
or mismatch in receptor-ligand complexes. |
| |
|
| PINTS
|
|
| PINTS finds reoccuring three-dimensional
patterns of amino acids. These amino-acids are close in
space but not necessarily close or co-linear in sequence,
for example the serine-protease catalytic triad. Unlike
other tools, PINTS does not aim to find proteins adopting
a similar fold. |
| |
|
| DynDom
|
|
| DynDom is a program to determine
domains, hinge axes and hinge bending residues in proteins
where two conformations are available. |
| |
|
| Flexweb
|
|
| FLEXWEB is the FRODA module
(Framework Rigidity Optimized Dynamics Algorithm) which
moves the static results of a FIRST6 analysis into the
realm of dynamics where we actually explore the conformational
space available to flexible regions. |
| |
|
| HINGEprot
|
|
| An algorithm for protein hinge
prediction using elastic network models. |
| |
|
| MultiBind
|
|
| Recognizes spatial chemical
binding patterns common to a set of protein structures. |
| |
|
| PIC
|
|
| Protein Interactions Calculator
(PIC) is a server which recognizes various kinds of interactions;
such as disulphide bonds, hydrophobic interactions, ionic
interactions, hydrogen bonds, aromatic- aromatic interactions,
aromatic-sulphur interactions and cation -? interactions
within a protein or between proteins in a complex. |
| |
|
| STITCH
|
|
| STITCH is a resource to explore
known and predicted interactions of chemicals and proteins.
Chemicals are linked to other chemicals and proteins by
evidence derived from experiments, databases and the literature. |
| |
|
| ProtMot
|
|
| This web site analyzes structure
of proteins and output the list of hydrogen bonding patterns
network motifs. The list of motifs, a superset of the
secondary structures, is shown both projected on the protein
structure and as a network motif significance profile
(SP), a chart which gives the occurrences of each motif
in the protein. |
| |
|
| GetArea
|
|
| Quite often a biomolecular researcher
wants to quickly calculate solvent accessible surface
area or solvation energy. |
| |
|
| ASAP
|
|
| ASAP predicts solvent accessible
surface area of proteins. Currently the Web predictor
only accepts single protein sequence as input. Please
select the type of protein and enter protein sequence
in FASTA format in the text area. |
| |
|
| RECCR
|
|
| The Rensselaer Exploratory Center
for Cheminformatics Research is dedicated to advancing
the field of Cheminformatics and increasing the availability
of new methods within the Cheminformatics user community. |
| |
|
| PROTEIN INTERACTIONS |
|
| |
|
| PIPSA
|
|
| This PIPSA service is provided
for the comparison of the electrostatic interaction properties
of proteins. It permits the classification of proteins
according to their interaction properties. PIPSA may assist
in function assignment, the estimation of binding properties
and enzyme kinetic parameters. |
| |
|
| MAPPIS
|
|
| Recognizes spatially conserved
chemical interactions shared by a set of PPIs. |
| |
|
| 121-Site
Engine |
|
| Surface and physico-chemical
alignment of proteinprotein interfaces. |
| |
|
| PROTORP |
|
| PROTORP server is a bioinformatics
tool designed to analyse the interfaces between protein
chains in protein-protein associations. |
| |
|
| MolSurfer
|
|
| MolSurfer is a graphical tool
that links a 2D projection of a macromolecular interface
to a 3D view of the macromolecular structures. |
| |
|
| AquaProt
|
|
| AquaProt analyses protein-protein
binding interface, defines inter-residue interaction map
within the interface and extracts related water molecules. |
| |
|
| VASCo
|
|
| VASCo is a program pipeline
including a visualization tool to calculate and visualize
annotated surfaces with special emphasis on surface contact
regions and protein-protein interactions. Crystal contacts
and biological contacts can be calculated based on surface
points. Molecular properties such as electrostatic potential
or hydrophobicity can be calculated and mapped on those
surface points. The molecular surfaces and properties
are calculated using existing established programs, which
are integrated into the package, as well as using own
developed programs. The modular pipeline can easily be
extended to include new properties for annotation. The
output of this pipeline is most conveniently displayed
in PyMOL as Compiled Graphics Objects (CGO) using a custom-made
plug-in. |
| |
|
| SPPIDER
|
|
| SPPIDER is a server for identification
of residues involved in protein-protein interactions. |
| |
|
| FoldX
|
|
| FoldX provides a fast and quantitative
estimation of the importance of the interactions contributing
to the stability of proteins and protein complexes. |
| |
|
| MUTATION |
|
| |
|
| SIFT
|
|
| SIFT predicts whether an amino
acid substitution affects protein function based on sequence
homology and the physical properties of amino acids. SIFT
can be applied to naturally occurring nonsynonymous polymorphisms
and laboratory-induced missense mutations. |
| |
|
| SNAP |
|
| Evaluating effects of single
amino acid substitutions on protein function |
| |
|
| CUPSAT
|
|
| CUPSAT is a tool to predict
changes in protein stability upon point mutations. The
prediction model uses amino acid-atom potentials and torsion
angle distribution to assess the amino acid environment
of the mutation site. Additionally, the prediction model
can distinguish the amino acid environment using its solvent
accessibility and secondary structure specificity. |
| |
|
| MUpro
|
|
| Prediction of Protein Stability
Changes for Single-Site Mutations from Sequences. |
| |
|
| PANTHER
|
|
| Estimates the likelihood of
a particular nonsynonymous (amino-acid changing) coding
SNP to cause a functional impact on the protein. |
| |
|
| RNA |
|
| |
|
| ConSurf
Server |
|
| A server for identification
of conserved regions in nucleotides. |
| |
|
| DIANA
LAB |
|
| The focus of the DIANA lab is
on the development of algorithms, databases and tools
for interpreting and archiving genomic data in the framework
of a systemic analysis. Current emphasis is on the analysis
of microRNA (miRNA) and protein coding genes. MiRNAs are
recently identified to be very abundant in mammalian organisms
and play a key role in regulating development. |
| |
|
| ORF
Finder |
|
| The ORF Finder (Open Reading
Frame Finder) is a graphical analysis tool which finds
all open reading frames of a selectable minimum size in
a user's sequence or in a sequence already in the database.
This tool identifies all open reading frames using the
standard or alternative genetic codes. |
| |
|
| Six
Frame Translation |
|
| Six frame translation of sequence. |
| |
|
| Webcutter
|
|
| Webcutter is a useful tool for
experimentors working with recombinant DNA. |
| |
|
| RepeatMasker
|
|
| The tool screens DNA sequences
in FASTA format against a library of repetitive elements
and returns a masked query sequence ready for database
searches. RepeatMasker also generates a table annotating
the masked regions. |
| |
|
| Reverse
Complement of Sequence |
|
| To find reverse complementary
sequences. |
| |
|
| Sequence
Cleaning Program |
|
| This program will take a protein
or nucleic acid sequence and delete Numbers, Space and
NewLine [enter/return] characters from the sequence. |
| |
|
| Shuffle |
|
| This program will take a protein
or nucleic acid sequence and shuffle the order of characters
to produce a randomized sequence with the same overall
composition as the original sequence. |
| |
|
| BioChemWeb.org
|
|
| Scientific databases and tools |
| |
|
| MOTIFS
|
|
| Tools and databases |
| |
|
| biophilessurf
|
|
| Databases of immunoinformatics |
| |
|
| Metabolomics
society |
|
| Metabolic databases. |
| |
|
| Dot
Matrix Plot |
|
| Dot or matrix plots provide
an easy and powerful means of sequence analysis, useful
for searching out regions of similarity in two sequences
and repeats within a single sequence. |
| |
|
| LALIGN
|
|
| LALIGN find internal duplications
by calculating non-intersecting local alignments of protein
or DNA sequences. |
| |
|
| SIM4
|
|
| SIM4 addresses the problem of
efficiently aligning a transcribed and spliced DNA sequence
(mRNA, EST) with a genomic sequence containing that gene,
allowing for introns in the genomic sequence (taking into
account consensus splice signals) and a relatively small
number of sequencing errors. |
| |
|
| FASTA
|
|
| DNA and protein sequence alignment
software package |
| |
|
| RNAfold
web server |
|
| The RNAfold web server will
predict secondary structures of single stranded RNA or
DNA sequences. |
| |
|
| EMBOSS
|
|
| A free Open Source software
analysis package specially developed for the needs of
the molecular biology (e.g. EMBnet) user community. The
software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence
data from the web. Also, as extensive libraries are provided
with the package, it is a platform to allow other scientists
to develop and release software in true open source spirit.
EMBOSS also integrates a range of currently available
packages and tools for sequence analysis into a seamless
whole. |
| |
|
| MSA |
|
| |
|
| PRALINE
|
|
| Multiple sequence alignment
tool. |
| |
|
| WBLOGO
|
|
| Generates sequence logos, graphical
representations of the patterns within a multiple sequence
alignment. |
| |
|
| T-ACE
|
|
| T-ACE was developed for the
analysis and organization of transcriptome projects but
is also helpful for the organization of small sequence
datasets e.g. extracts of a large transcriptome databases. |
| |
|
| PHYLOGENETIC ANALYSIS |
|
| |
|
| PAUP
|
|
| PAUP version 4.0 is a major
upgrade and new release of the software package for inference
of evolutionary trees, for use in Macintosh, Windows,
UNIX / VMS, or DOS-based formats. The influence of high-speed
computer analysis of molecular, morphological and/or behavioral
data to inter phylogenetic relationships has expanded
well beyond its central role in evolutionary biology,
now encompassing applications in areas as diverse as conservation
biology, ecology, and forensic studies. |
| |
|
| PHYLIP
|
|
| A free computational phylogenetics
package of programs for inferring evolutionary trees. |
| |
|
| Phylodendron
|
|
| For drawing phylogenetic trees. |
| |
|
| TreeView
|
|
| TreeView is a simple program
for displaying phylogenies on Apple Macintosh and Windows
PCs. |
| |
|
| DAMBE
|
|
| Software package for extensive
data analysis in molecular biology and evolution, for
Windows ME/2000/XP/VISTA and Linux. |
| |
|
| PHASE
|
|
| Package that performs molecular
phylogenetic inference. |
| |
|
| ArboDraw
|
|
| A program for building and displaying
phylogenetic trees of protein and nucleic acid sequences. |
| |
|
| Jevtrace
|
|
| Jevtrace is a Java implementation
of the evolutionary trace method. |
| |
|
| NJplot
|
|
| NJplot is a tree drawing program
able to draw any phylogenetic tree expressed in the Newick
phylogenetic tree format (e.g., the format used by the
PHYLIP package). NJplot is especially convenient for rooting
the unrooted trees obtained from parsimony, distance or
maximum likelihood tree-building methods. |
| |
|
| IMGT
web resources |
|
| The IMGT Immunoinformatics page
comprises links to databases, tools and resources on immunoglobulins
(IG) or antibodies, T cell receptors (TR) and major histocompatibility
complex (MHC). |
| |
|
| PHENOMICS |
|
| |
|
| PROPHECY
|
|
| A yeast phenome database. |
| |
|
| InterPhenome
|
|
| An established portal that allow
phenome data to be collectively searched for phenotypes
and associated information. |
| |
|
| METABOLOMICS |
|
| |
|
| hmp
|
|
| The Human Metabolome Database
(HMDB) is a freely available electronic database containing
detailed information about small molecule metabolites
found in the human body. It is intended to be used for
applications in metabolomics, clinical chemistry, biomarker
discovery and general education. |
| |
|
