RNA/DNA:

The RNA World	The RNA World website at IMB Jena Biocomputing Group (DE)
Vienna RNA	Vienna RNA Package: RNA Secondary Structure Prediction (UNIVIE, AT)
NDB	The Nucleic Acid Database (NDB)
RNAbase	The RNA Structure Database
SCOR	SCOR: Structural Classification of RNA
JENA-RNA	Index of RNA structures at "Jena Library of Macromolecules"

INSDC	International Nucleotide Sequence Database Collaboration
GenBank	Genbank, the NIH genetic sequence database.
EMBL	The EMBL Nucleotide Sequence Database (EMBL-Bank)
DDBJ	DDBJ, DNA Data Bank of Japan

Genomes:

COGs	Clusters of Orthologous Groups of proteins: Phylogenetic classification of proteins encoded in complete genomes
GenProtEC	GenProtEC: database dedicated to E. coli genome and proteome
JCVI	J. Craig Venter Institute.
GOLD	GOLD: Genomes OnLine Database HomePage
GenomeNet	GenomeNet WWW server (KEGG, DBGET, ...)

Tools for GENE detection and modeling:

RepeatMasker	Masking repeats and low complexity DNA sequences.
Censor	CENSOR - a program for identification and elimination of repetitive elements from DNA sequences.
CodonW	Codonw: Correspondence Analysis of Codon Usage
C.U.D.	Codon Usage Database
S.M.S.	The Sequence Manipulation Suite for analyzing and formatting DNA and protein sequences.
Promoter Scan	Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.
Promoter 2.0	Promoter 2.0 predicts transcription start sites of vertebrate PolII promoters in DNA sequences
NetStart 1.0	The NetStart server produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences
AUG	AUG_EVALUATOR for start codons prediction
CpG Plot	Detection of regions of genomic sequences that are rich in the CpG pattern

Tools for GENE prediction:

GeneMark	GeneMark.  A family of gene prediction programs
ORF Finder	ORF Finder (Open Reading Frame Finder)
FramePlot	Predicts protein-coding region of high G+C content bacterial DNA, such as Streptomyces
Glimmer	Glimmer uses interpolated Markov models (IMMs) to identify coding regions.
GENSCAN	Identification of complete gene structures in genomic DNA
NetGENE	The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.
HMMgene	HMMgene: Prediction of vertebrate and C. elegans genes.
Genie	Genie: Gene Finder Based on Generalized Hidden Markov Models in Drosophila
GeneId	GeneId is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. (Roderic Guigo's Lab).
MetaGene	MetaGene 2.7 is a powerful tool designed to provide exhaustive analysis of predicted gene features in sequence.
Webgene	Webgene: tools for prediction and analysis of protein-coding gene structure.

Genome guides:

NCBI-HumanGenome	Human genomic sequence and gene annotation at NCBI.
UCSC Genome	Genome Bioinformatics at University of California at Santa Cruz.
Ensembl	Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes.

FBS	FRONTIERS IN BIOSCIENCE; DNA/RNA ANALYSIS TOOLS
Deambulum	The DEAMBULUM (Computing applied to biomolecules and genomes) : nucleic acid sequence analysis

Primary structure.
 

MyHITS	Prosite & Pfam Motif Scan Server (ISREC, CH)
ProDom	ProDom protein domain database (INRA, FR)
InterPro	Integrated resource of protein domains and functional sites. (EBI, UK)
PFAM	Protein families database of alignments and HMMs (Sanger, UK)
CDART	Conserved Domain Architecture Retrieval Tool  (It shows similar domain achitectures, too) (NCBI)
PRINTS	Protein Motif Fingerprint Database (UCL, UK)
SMART	Simple Modular Architecture Research Tool. Domains/motif  detection (EMBL)
SignalP	Predicts the presence and location of signal peptide (CBS, DK)

 

PredictProtein	The PredictProtein server  (Columbia, USA)
ExPASy Tools	ExPASy Proteomics tools

Protein families / classification.
 

COG	Phylogenetic classification of proteins encoded in complete genomes (NCBI)
ProtoMap (not updated)	An automatic hierarchical classification of all swissprot proteins (not updated)
Search and Cluster (not updated)	Recursive BLAST-searches and NCUT-clustering (PDG-CNB)

 

PFAM-UK	Protein families database of alignments and HMMs (Sanger, UK)
PFAM-USA	Protein families database of alignments and HMMs (Washington D.C. (USA))
PFAM-Sweden	Protein families database of alignments and HMMs (Karolinska Institutet, Sweden)
InterPro	Integrated resource of protein domains and functional sites. (EBI, UK)
ProDom	ProDom protein domain database (INRA, FR)

Secondary structure.
 

EVA-CUBIC	EVA, evaluation of protein structure prediction servers in 'real time'. CUBIC, Columbia Univ, New York.
EVA-CNB	EVA, evaluation of protein structure prediction servers in 'real time'. CNB, Madrid.

TMHMM	Prediction of transmembrane helices in proteins (CBS, DK)
HMMTOP	Prediction of transmembrane helices and topology of proteins (Inst. Enzymol. Budapest)
SignalP	Predicts the presence and location of signal peptide (CBS, DK)
COILS	Prediction of Coiled Coil Regions in Proteins (ISREC, CH)
Parcoil2	Paircoil2 predicts the parallel coiled coil fold from sequence. (MIT, USA)
MultiCoil	Program to distinguish between dimeric and trimeric Coiled Coils (OSC, USA)
Jpred	A consensus method for protein secondary structure prediction (EBI, UK)
Psi-Pred	Protein structure prediction server  (secondary structure & transmembrane topology) (University College London, UK)
APSSP2	APSSP2: Advanced Protein Secondary Structure Prediction Server (Chandigarh, INDIA)
TOPS	Topology of Protein Structure (Univ. of Leeds)
SAM-T06 / T02	SAM-T06 / SAM-T02 secondary structure prediction.

PredictProtein	The PredictProtein server  (Columbia, USA)
ExPASy Tools	ExPASy Proteomics tools

3D structure / Modeling / Threading

Homology modelling:
 

EVA-CUBIC	EVA, evaluation of protein structure prediction servers in 'real time'. CUBIC, Columbia Univ, New York.
EVA-CNB	EVA, evaluation of protein structure prediction servers in 'real time'. CNB, Madrid.

Swiss-Model	SWISS-MODEL. An Automated Comparative Protein Modelling Server (ExPASy, CH)
SWISS-MODEL Repository	SWISS-MODEL Repository. A database for theoretical protein models (ExPASy, CH)
MODELLER	MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (UCSF)
ModBase	ModBase: a database of three-dimensional protein models calculated by comparative modeling (UCSF)
WHATIF	WHAT IF  Web interface:  homology modelling, drug docking, electrostatics calculations, structure validation and visualisation.
TITO/Modeller	Modeller at the CBS Bioinformatic Tools Server (Montpellier, France)
CPHmodels	The CPHmodels Server using comparative (homology) modelling (BioCentrum, Denmark)
3D-JIGSAW	Automated system to build three-dimensional models for proteins. (Cancer Research UK)
Loops Database	Protein Loop Classification. (Cancer Research UK).
Rotamers	Rotamer Libraries. Richardson Lab. Duke University.

Threading:
 

EVA-CUBIC	EVA, evaluation of protein structure prediction servers in 'real time'. CUBIC, Columbia Univ, New York.
EVA-CNB	EVA, evaluation of protein structure prediction servers in 'real time'. CNB, Madrid.

PredictProtein	The PredictProtein server (TOPITS) (Columbia, USA)
3D-PSSM/Phyre	3D-PSSM & Phyre Protein Fold Recognition (Threading) Server (Imperial Cancer Res. Fund., UK)
UCLA-DOE	UCLA-DOE Fold-Recognition server (UCLA, USA)
Psi-Pred (GenThreader)	Protein structure prediction server  (sequence profile based fold recognition) (University College London UK)
SAM-T06/T02	SAM-T06 / SAM-T02 protein structure HMM library search.
FFAS	Fold & Function Assignment System. (Burnham Institute, USA)
FUGUE	FUGUE Profile Library Search Against HOMSTRAD (Cambridge, UK)
Threading Meta-Server	Threading Meta-Server at the CBS Bioinformatic Tools Server (Montpellier, France)
LOOPP	A program for potential optimization and alignments (Cornell, USA)
Superfamily	HMM library and genome assignments server (Cambridge, UK)

Structure validation:

AQUA	AQUA - Alignment Quality Assessment
BIOTECH Validation Suite	Biotech Validation Suite for Protein Structures (PROCHECK, PROVE & WHAT IF)
WHATIF	WHAT IF  Web interface:  homology modelling, drug docking, electrostatics calculations, structure validation and visualisation.
3D Evaluation	Verify3D & PROSA II at the CBS Bioinformatic Tools Server (Montpellier, France)

Databases:

PDB - RCSB	Protein Data Bank (RCSB)
PDBsum	Summaries and structural analyses of PDB data files (UCL, UK)
Get ExPDB	Get ExPDB entries for a PDB code (Swiss-Model, ExPASy, CH)
OCA	PDB advanced browser(EBI)
EC->PDB	Enzyme Structures deposited in PDB (EBI, UK)
Prosite->PDB	PROSITE patterns in PDB entries (EBI, UK)
Ligands->PDB	List of ligands bound to PDB structures (EBI, UK)
RELIBASE	Relibase: A program for searching protein-ligand databases.
NDB	The Nucleic Acid Database Project (UK) (Nucleic Acid Structures)
IMB Jena	IMB Jena Image Library of Biological Macromolecules (Jena, Germany)
RNAbase	The RNA Structure Database
SCOR	SCOR: Structural Classification of RNA
JENA-RNA	Index of RNA structures at "Jena Library of Macromolecules"

CORINA

CORINA: A powerful and reliable tool for the generation of 3D atomic coordinates (Molecular Networks GmbH, Germany)

SCOP	Structural Classification of Proteins (MRC-LMB, UK)
CATH	CATH Protein Structure Classification (UCL-BSM, UK)
The Dali server	The Dali server: Network service for comparing protein (query) structures in 3D (EBI)
FSSP	Dali Fold Classification of Proteins (FSSP) (Biocenter, Helsinki)
DaliDD	Dali Domain Dictionary: structural classification of protein domains (EBI)
Homstrad	Homologous Structure Alignment Database (CrystBioc, UK)

Contacts & Quaternary structure
 

EVA-CUBIC	EVA, evaluation of protein structure prediction servers in 'real time'. CUBIC, Columbia Univ, New York.
EVA-CNB	EVA, evaluation of protein structure prediction servers in 'real time'. CNB, Madrid.

PDGcon

Prediction of residue contacts in proteins based on correlated mutations. CSB-CNB, Madrid.

3D Complex	A Database for protein complexes of known 3-dimensional structure. (MRC Laboratory of Molecular Biology. UK)
PQS	Protein Quaternary Structure Database Searches at the EBI
NDB	The Nucleic Acid Database Project (UK) (Protein/Nucleic Acid Complexes)

 
 

Perl:
 

Bioperl Project	Open source Perl tools for bioinformatics, genomics and life science research
Perl5 Guide	Rex Swain's HTMLified Perl 5 Reference Guide
www.perl.com	The Source for Perl - Home Page
Perl tutorials	Perl tutorials at www.perl.com
Perl Guide	A Practical Perl Guide
CPAN	Comprehensive Perl Archive Network

 

 

2007

BIOWEB: MOLECULAR MODELLING GROUP Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM). http://www.cbm.uam.es/bioweb

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