BETRAN LAB

Evolutionary Biology

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PROTEINS

[Protein Identification & Characterization] [Sequence Comparison, Homology-Identity Analyses] [Keyword Search & Data Retrieval Servers][ Sequence Motifs/Patterns Recognition and Analysis] [Protein Domains/Motifs/Patterns Databases] [Sequence Alignment Servers & Databases] [Multifunction Protein Sequence Analysis Tools] [Sequence Presentation Tools] [Structure Prediction & Modeling] [Physico-Chemical Analysis of Protein Structures] [Protein Structure & Information Databases] [On-Line Structure Viewing] [Database Information Retrieval Servers] [Protein Structure: Projects & Initiatives ]

Protein Identification & Characterization
AACompSim Compares the amino acid composition of a SWISS-PROT entry with all other entries.
TagIdent Get the SWISS-PROT proteins closest to a given pI and Mw and identify proteins with a sequence tag.
Propsearch A sequence property approach to searching protein databases.
Compute pI/Mw Compute the theoretical pI and Mw from a SWISS-PROT or TREMBL entry or for a user sequence.
ProteinProspector A variety of tools from UCSF (MS-Fit, MS-Tag, MS-Digest, etc.). For mining sequence databases in conjunction with Mass Proteometry experiments.
MultiIdent Identifies proteins with pI, MW, amino acid composition, sequence tag and peptide mass fingerprinting data.
PeptideMass Calculate masses of peptides and their posttranslational modifications for a SWISS-PROT or TREMBL entry or for a user sequence.

Sequence Comparison & Homology Analyses

Sequence Homology Analysis

AbCheck Kabat Database with Query Sequence Search.
BEAUTY BLAST Enhanced Alignment Utility.
PSI-BLAST BLAST® (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
BLOCKS Database Query sequence comparison against the BLOCKS database of highly Conserved Regions of Protein.
FASTA Pearson and Lipman(Algorithm)Sequence Comparison Service.
FASTAPAT FASTA -based PIMA (Pattern-Induced Multiple Sequence Alignment) Database.
PepPepSearch Search SwissProt Database for a Protein Sequence.
PPSearch Protein motifs or fingerprint searches.
ProfileScan Server Sequence Search against Seq Profiles Database.
PROPSEARCH Compositional search using a sequence.

Gene Search Using a Protein Sequence

Protein Search Using a Nucleotide Sequence
Darwin An interactive tool for peptide and nucleotide sequence analysis.

Keyword Search & Data Retrieval Servers
ENTREZ Protein Database Searching Server.
ProteinInfo Search Protein Databases.
Species-Specific Protein Sequence Search
SCANPS Very fast implementation of the true Smith & Waterman algorithm for protein database searches.
SRS6 Database searching using the Sequence Retrieval System version 6.

Sequence Motifs/Patterns Recognition & Analysis

Search Protein Sequence DB for Query Motif

BLASTPAT Search of a Pattern Database with a Query Protein Sequence..

General Multi-Motif Search

FASTA-PAT Search of a Pattern Database with a Query Protein Sequence.
HMM Search Motif Search of a Protein Sequence using the Pfam-A Database of Protein Domains.
MEME Multiple EM for Motif Elicitation.
MOTIF Pattern Search Service.
PatternFind Pattern Search of SwissProt and GenPept Protein Sequence Databases.
Pratt Pattern Discovery Tool.
PRINTS/PROSITE Scanner Search the PRINTS and PROSITE Databases with Query Sequence.
ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
ProfileScan Compare a sequence against PROSITE Motifs Database.
PROSITE Search Profile Motifs Searches of ProSite Database.
Network Protein Sequence @nalysis
Search Pattern Search for Sequence Pattern.
SPAPD Screening Pattern or Alignment against a Protein databank.
SwissShop ProSite Information Query Service.

Peptide Binding Prediction

HLA Peptide Motif Search HLA Peptide Binding Predictions.

Post-Translation Modification

NetOglyc Search query sequence for potential O-glycosylation sites.
PhosphoBase Protein Phosphorylation Site Sequence Database.

Signal Peptide Motifs

SignalP Predict Signal Peptide Cleavage Sites.

Transmembrane Spanning Motifs

DAS Transmembrane Prediction from a Query Sequence.
Predict Protein Protein Structure Prediction.
SOSUI Prediction of Transmembrane Regions.
TMPRED Protein Transmembrane Region Prediction.
TopPred2 Topology Prediction of Membrane Proteins.

Transcriptional Factors/Elements

TFSEARCH Transcription Factor Search.
The Sequence Manipulation Suite

Protein Domains/Motifs/Patterns Databases

AnDom Annotation of Domains.
PFAM Protein families databases (HMM derived).
PRINTS Protein Motif Fingerprint Database.
PRODOM Protein Domain Database.
Prosite (ExPASy) Protein families and domains.
SBASE Database of Annotated Protein Domain Sequences.

Sequence Alignment Servers & Databases

Sequence Alignment Analyses

ALIGN Global Alignment of Two Sequences.
AllAll Server multi-allignment function.
AMAS Analyze multiply aligned sequences.
Block Maker Server Finds Blocks (short multiply aligned ungapped segments of highly conserved regions) in Groups of Related Protein Sequences.
CLUSTALW Multiple Sequence Alignments.
DbClustal Global multiple alignments of protein sequences detected by DB searches.
LALIGN N-Best Two Sequence Local Alignment.
MAP Multiple Global Alignment of Sequences Using Iterative Pairwise Method.
Match-Box Multiple Sequence Alignment.
MSA 2.1 Multiple Sequence Alignment.
Multalign Multiple Sequence Alignment Service.
MUSCLE MUltiple Sequence Comparison by Log-Expectation
Pairwise Sequence Alignment
PIMA Pattern-Induced Multiple [Sequence] Alignment.
SIM + LALNVIEW Alignment of two protein sequences with SIM.
Swiss-Shop Swiss-Shop is a service that , allows you to automatically obtain (by email) new sequence entries relevant to your field(s) of interest.
T-COFFE Computes a multiple sequence alignment and the associated phylogenetic tree.

Global and Domain Similarity Search

Protein Information Resource (PIR)

Multi-Function Protein Sequence Analysis Tools

Biology Workbench v3.2
DARWIN Data Analysis and Retrieval With Indexed Nucleotide & Peptide Sequences
SAPS Statistical Analysis of Protein Sequences.
The Sequence Manipulation Suite

Sequence Presentation Tools

BOXSHADE Pretty Printing and Shading of Multiple-Alignment Files.
Laln View.

Structure Prediction & Modeling Services

2D & 3D Structure Prediction Analyses

3D-PSSM Protein Fold Recognition Using 1/3D Sequence Profiles with 2D Info.
AGADIR Protein Helical Content Predictor.
CE 3D Structure Comparison & Alignment..
COILS Prediction of Coiled Coiled Regions.
COMPARER ON-LINE Protein Structure Superposition Comparison.
DALI Structure-to-Structure Comparison using Structures Modeled from PDB and User-Supplied Structure Coordinates.
DPM Secondary Structure Prediction.
FoReSST Fold Recognition from Secondary Structure.
FUGUE Structure Profile Library Search against HOMSTRAD Database.
GARNIER Secondary Structure Prediction.
GIBRAT Secondary Structure Prediction.
GOR IV Secondary Structure Prediction.
Helix-Turn-Helix HTH Motif Prediction.
GRASP Graphical Representation and Analysis of Structure Server.
HNNSSP Hierarchical Neural Net Secondary Structure Prediction.
JOY Protein Structure & Alignment Analysis.
MFOLD
MLRC Secondary Structure Prediction.
nnPredict Secondary Structure Prediction.
PHD
Phyre Protein Homology/analogY Recognition Engine
PREDATOR Secondary Structure Prediction.
PredictProtein Secondary Structure Prediction.
PROF Secondary Structure Prediction System.
Protein Fold Recognition Server Prediction of Structural Folds in Proteins.
ProtParam Physico-chemical parameters of a protein sequence (composition, extinction coefficient, etc.)
ProtScale Secondary Structure Properties Prediction.
PSA Protein Sequence [Structure Prediction] Server.
QLSSP (w/o Homologuous Sequences) Quadratic Logistic Secondary Structure Prediction.QLSSP (w/ Homologuous Sequences)
RandSeq Random protein sequence generator.
SIPMA96 HOMOLOGUE Secondary Structure Prediction.
SAWTED Structure Alignment With Text Description.
SOPM Self Optimized Prediction Method for Secondary Structure Prediction Service.
SOPMA SOPM Secondary Structure Prediction.
SSCP-AA Secondary Structure Prediction from Amino Acid Composition.
SSCP-Seq Secondary Structure Prediction from Protein Sequence.
Swiss-Model Protein Modeling Server.
VAST Structure-Structure Similarity Search.

3D Protein Structure Comparison & Analysis

ERRAT Protein Structure Verification.
MaxSprout Reconstruction of 3D coordinates from C(alpha) trace.
MolSurfer Navigating Protein-Protein Interfaces.
SwissModel Automated Protein Modeling.
TOPS Protein structural topology.
ENTREZ Biomolecule 3D Structure Search Biomolecule 3D Structure Search.
PQS Protein quaternary structure query.

Physico-Chemical Analysis of Protein Structures

ASC Analytic Surface Calculation of PDB Protein Structures.

Protein Structure & Information Databases
BioMagResBank Database of NMR-derived Protein Structures.
CAMPASSCAMbridge DB of Protein Alignments organized as Structural Superfamilies.
CATH Protein Structure Classification.
Culled PDB Unique/Representative Proteins in the PDB.
The Dali Database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
DIP Database of Interacting Proteins.
ENTREZ Structure Biomolecule 3D Structure Search.
Enzyme Structure Database
HAD Heavy Atom Databank.
HOMSTRAD Homologous Structure Alignment Database.
MMDB ENTREZ Molecular Modeling Database.
Merops The Peptidase Database.
MolMovDB Database of Macromolecular Movements.
PDB Protein Database of 3-D Structures of Biological Macromolecules.
PDBLite
PIR Protein Information Resource Database.
PMD Protein Mutant Database.
Protein Loop Classification
Protein Databank in Europe (PDBe) Macromolecular Structures Database.
Protein Disease Database (PDD)
Protein Kinase Resource is a web accessible compendium of information on the protein kinase family of enzymes.
SCOP Structural Classification of Proteins Database.
SLoop Database of Super Secondary Fragments.
Swiss-2Dpage Two-dimensional polyacrylamide gel electrophoresis.
SWISS-MODEL Repository Automatically generated protein models database.
SWISS-PROT Protein sequences.
The OWL database Non-redundant protein database.

PDB Search & Browse Resources

PDB BROWSER
PDB-Select Database is a Subset of the Structures of PDB entries containing (Non)-Homologous Sequences.
PDBFINDER An abbreviated database of PDB, DSSP, and HSSP Entries.
PDB Search (DBGET)
PDBSTR Reorganized format PDB Database.
PDBsum Summaries and structural analyses of all PDB entries.
PDB-At-A-Glance Hierarchal Glance at PDB Entries.

On-Line Structure Viewing

Protein Explorer Protein Structure Explore Tool.
WebMol Java PDB Viewer.

Database Information Retrieval Servers

ENTREZ Biomolecule 3D Structure Search.

Protein Structure: Projects & Initiatives

JCSG Joint Center for Structural Genomics
PPA Proteome of Pyrobaculum Aerophilum
PSI Structural Genomics Initiative
S2F Structure 2 Function
SGRC Structural Genomics Research Consortium


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