Pedro's BioMolecular Research Tools

This is a completely outdated mirror of Pedro's Molecular Biology Search and Analysis Tools. This copy resides on the MBCF/DFCI web site.
You can google again but I do not think Pedro has updated these links since 1995.

Go to CMS Molecular Biology Resource for a better list although this is also getting slightly out of date. An advanced Google search might be the best way to go.

"Pedro" is Pedro Maldonado Coutinho, a graduate student at Iowa State University of Science and Technology.
Pedro's personal Classification of Links:
*1* - Hot/Very Useful Tools *
*2* - Good/Useful Tools *
dot - Other Tools *
* - Journal Links *
[L] - Local Pages *
[E] - e-mail Search *
!New! - More Recent Additions/Changes *
!Recent! - Less Recent Additions/Changes *

(W3) - WWW Server *
(Gopher) - Gopher Server *
(FTP) - FTP Server *
(Telnet) - Telnet Port *


Molecular Biology Search and Analysis

dot 3D-ALI - Database relating Proteins Structures and Sequences (see Documentation) at EMBL-Heidelberg W3
dot AA Analysis [E] - Protein Identification in SwissProt and PIR using Amino Acid Composition at EMBL-Heidelberg W3
dot AA CompIdent - Protein Identification in SwissProt using Amino Acid Composition at ExPASy, Switzerland W3
dot AA CompSim - Compare the Amino Acid Composition of a SwissProt Entry with Other Entries at ExPASy, Switzerland W3
line AA Sequence Analysis - Multiple Analysis of a Native or Modified Amino Acid Sequence at Rockefeller U. W3
dot AbCheck - Test an Antibody Sequence Against the Kabat Database at U. College-London, UK W3
*2* ALIGN - Optimal Global Alignment of Two Sequences with No Short-cuts at EERIE-Nimes, France and Align at MIPS, Germany W3
*2* AllAll[E] - Relationships in a Set of Related Peptides at ETH-Zürich, Switzerland W3
*2* AllAllDB[E] - Search the All-Against-All Database of SwissProt at ETH-Zürich, Switzerland W3
*2* AMAS - Analysis of Protein Multiple Sequence Alignments at U. Oxford, UK W3
dot ASC[E] - Analytic Surface Calculation of PDB Protein Structures at EMBL-Heidelberg W3
*2* ATLAS!New! - Search DNA and Protein Sequence Databases at MIPS, Germany W3
*1* BCM Search Launcher at Baylor College of Medicine W3
*2* BEAUTY - BLAST Enhanced Alignment Utility (see Documentation) at Baylor College of Medicine W3
*1* BERLIN - RNA Databank of 5S rRNA and 5S rRNA Gene Sequences at CAOS/CAMM, The Netherlands W3
*1* BIOACCELERATOR at Weizmann Institute of Science, Israel W3
*1* bioCUSI - Multiple Access to Biological Servers at OCMS-Oxford W3
*2* Biological Units - Expanded PDB Entries with Full Biological Units at Brookhaven National Laboratory FTP
*2* Biologist's Search Palette - Collection of Search Engines for Biological Databases at Oxford U., UK W3
*1* BLAST - Basic Local Alignment Research Tool at NCBI, BLAST (hiv, vector, etc) at Stanford U., BLAST at GenomeNet, Japan, BLAST at EERIE-Nimes, France, BLAST[E] at CRIHAN, France BLAST (with Entrez and SRS Links) at Baylor College of Medicine and BLAST at EPFL, Switzerland W3
*2* BLASTPAT - BLAST-based Pattern Database Search (see Documentation) at Baylor College of Medicine W3
*1* BLITZ[E] - Fast comparison of protein sequences against SwissProt (see Documentation) at EBI, UK W3
*2* BLOCKS - Database of Highly Conserved Regions in Proteins W3 and BLOCKS-WAIS Gopher at Fred Hutchinson Cancer Research Center, BLOCKS at EMBL-Heidelberg W3
*2* BioMagResBank - A Database of NMR-Derived Protein Structures at BIMAS-NIH W3
*2* BioSCAN - Biological Sequence Comparative Analysis at U. North Caroline W3
*2* BMCD - Biological Macromolecule Crystallization Database at CARB W3
*2* BOXSHADE - Pretty Printing and Shading of Multiple-Sequence Alignments at ISREC, Switzerland W3
*2* CATH - Protein Structure Classification at UCL-London, UK W3
*2* CLUSTALW - Multiply Sequence Alignments at IBC-Washington U. W3
dot Codon Usage - Analysis of Different ORFs in a Gene Sequence at U. Minnesota W3
*2* Coils - Prediction of Coiled Coil Regions in Protein Sequences at ISREC, Switzerland W3
*1* CpGIsle - CpG Islands Database at BEN, Belgium W3
*2* Darwin[E] - Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences at ETH-Zürich, Switzerland W3
*2* dbEST - Database of Expressed Sequence Tags at NCBI W3
*1* DBGET - Integrated Database Retrieval System (w/ diagram links) at GenomeNet, Japan W3
dot DDBJ - DNA Database of Japan at National Institute of Genetics, Japan Gopher
dot Dot Plot - Compare a DNA Sequence with Itself at U. Minnesota W3
dot DrugBank!New! - Three-dimensional Drug Structure Databank at NIH W3
*2* DSSP - Database of Secondary Structure of Proteins from PDB (see Documentation) at EMBL-Heidelberg W3
*2* EC Enzyme at Johns Hopkins and EC Number Table at GenomeNet, Japan and GenoBase Enzyme Index at NIH W3
dot ECDC - E. coli Database Collection at Uni-Gießen, Germany W3
*2* EMBL - Nucleotide Sequence Database and EMBL-New Entries at EMBnet-Basel Gopher
*2* EMNEW - Index of New EMBL Sequences at EBI, UK W3
*2* EMP Compound and EMP Pathways - Selkov Enzyme and Metabolic Pathway (EMP) Database at NIH W3
*1* EMP Metabolic Pathways - Navigation in Metabolic Pathways from MCS-Computational Biology at Argonne National Laboratory W3
*1* ENTREZ - Protein and Nucleotide Database (see Documentation) at NCBI W3
*1* ENZYME - The Enzyme Data Bank at ExPASy, Switzerland W3
*2* Enzyme Structures Database - Structures of Enzymes Deposited in the PDB at UCL-London, UK W3
dot EPD - Eucaryotic Promoter Database at EMBL-Heidelberg, Germany and EPD at GenomeNet, Japan W3
dot EPO - European Patent Office Nucleotide Database at BiO/U. Oslo, Norway W3 and EPO at CSC, Finland Gopher
*1* FASTA[E] - Compare a Nucleic Acid Sequence to Nucleotide Sequence Databases (w/ updates) at EBI, UK, FASTA (Berlin, Vectorbank, etc) at Stanford U., FASTA at EERIE-Nimes, France and FASTA[E] at CRIHAN, France W3
*2* FASTPAT - FASTA-based Pattern Database Search (see Documentation) at Baylor College of Medicine W3
*2* FlyBase - Genetic and Molecular Database for Drosophila at Harvard U. W3
dot FSSP - Database of Families of Structurally Similar Proteins derived from PDB at EMBL-Heidelberg W3
*2* FTHOM[E] - Compare Protein Domain Homology at ABC, Hungary W3
*1* GDB - Human Genome Data Base at Johns Hopkins W3
*1* GenBank Database (+Updates) at NCBI and GenBank-Fetch at Washington U. W3
*2* Gene Finder - Predict Gene Structure, Internal Exons and Splicing Sites in DNA and Exon-Exon Junstion in cDNA at Baylor College of Medicine W3
dot GenLang - Find Genes and Other Higher-Order Features in Nucleotide Sequences at CBIL-U. Pennsylvania W3
*1* GenoBase at NIH W3
*1* Genome Databases and Genome Centers - World Wide Links at EERIE-Nimes, France W3
*2* Genome Workstation - Genome Related Links at Roslin Institute, UK W3
*1* Genomic Maps - Links to Genome Specific Resources at Biotech-Indiana W3
*1* GenQuest - Search Against Protein Databases with the Q server at Johns Hopkins W3
*1* Grail - Analysis of the Protein Coding Potential of a DNA Sequence (see Documentation) at ORNL W3
*1* GSDB - Genome Sequence Database at NCGR W3
dot GuessProt - Selects SwissProt proteins given pI and Mw at ExPASy, Switzerland W3
*2* HHS - SwissProt and PDB Systematic Sequence Classification Database at Washington U. W3
dot HOVERGEN - Database of Homologous Vertebrate Genes at CAOS/CAMM, The Netherlands W3
dot HPT - Protein Sequence Pattern Recognition in the PIR Database and HPT-Homology at MIPS, Germany W3
dot HSSP - Database of Homology-Derived Structures of Proteins based on PDB and SwissProt at EMBL-Heidelberg W3
*2* Kabat - Database of Proteins of Immunological Interest at Johns Hopkins Gopher
dot Kinemage-Index - "Kinetical Images" by Protein Type at Protein Science W3
dot Klotho - Biochemical Compounds Declarative Database at Washington U. W3
*2* LALIGN - Calculates the N-Best Local Alignments Between Two Sequences at EERIE-Nimes, France W3
*2* LFASTA - Local Similarity Searches Between Two Sequences Showing Local Alignments at EERIE-Nimes, France W3
*1* LIGAND - Ligand Chemical Database for Enzyme Reactions at GenomeNet, Japan W3
dot LiMB - Listing of Molecular Biology Databases at NIH Gopher and LiMB at EMBL-Heidelberg W3
*2* MassSearch[E] - Search SwissProt or EMBL Databases by Protein Mass After Digestion at ETH-Zürich, Switzerland W3
*2* Metabolic Database - Metabolic Reactions and Pathways at CGSC-Yale U. and Metabolic Database at INRA-Moulon, France W3
*2* MGD - Mouse Genome Database at Jackson Laboratory W3
dot MHCPEP - Database of Major Histocompatibility Complex (MHC) Binding Peptides at WEHI-Melbourne, Australia Gopher
dot MIPS-Alert - Automated Sequence Information Queries at MIPS, Germany W3
*1* Molecules R US - Interactive Text and Images of PDB Files at NIH W3
dot MPBD - Molecular Probe Data Base at EMBL-Heidelberg W3 and MPDB at U. Agricultural Sciences, Sweden Gopher
*2* MOOSE - Macromolecular Object Oriented Search Engine to Extract PDB Contained Information at Columbia U. W3
*2* MSA - Multiple Sequence Alignment at Washington U. W3
*1* MOTIF - Search Patterns in Protein Sequences at GenomeNet, Japan Motif[L][E] at GenomeNet, Japan w/ search from Iowa State W3
*2* Multiple Sequence Alignments - CLUSTAL-W, MAP, and PIMA alignments at Baylor College of Medicine W3
*2* NDB - Nucleic Acid Database at Rutgers U. W3
*1* nnPredict - Predict Protein Secondary Structure at UCSF and nnPredict[L][E] at w/ search from Iowa State W3
*1* NRL_3D - Sequence/Structure Database derived from PDB at Johns Hopkins and NRL_3D at EMBL-Heidelberg W3
dot NRSub - A Non-Redundant DNA Sequence Database for Bacillus subtilis at National Institute of Genetics, Japan W3
*2* NuclPepSearch[E] - Search SwissProt for a Nucletide Sequence at ETH-Zürich, Switzerland W3
*2* NYC-MASS - Protein Mass Spectrometry Database at Rockefeller U. W3
dot OBSTRUCT[E] - Correlate Sequence Subsets of PDB Protein Structures at EMBL-Heidelberg W3
*2* OMIM - Online Mendelian Inheritance in Man at Johns Hopkins W3
dot Organelle Genome - A Sequence Database at U. Montreal Gopher
*1* Organisms and Strains - Links to Databases Specific to Organism and Cell Collections at Biotech-Indiana W3
*1* OWL - Non-Redundant Protein Sequence Database (Updated Daily) at Johns Hopkins and OWL at UCL-London, UK W3
*2* PatScan[E] - Look for Pattern Matches in DNA or Protein Sequences at Argonne National Laboratory W3
*2* PatternFind[E] - Search the SwissProt and Genpept Protein Sequence Databases with a PROSITE-formatted Pattern at ISREC, Switzerland W3
*2* PDD - Protein Disease Database at NIMH-NCI W3
*1* PDB-Browser, PDB-Index and PDB-Pending - Protein Data Bank Structures at Brookhaven National Laboratory, PDB at GenomeNet Japan, PDB at U. Genova, Italy, PDB-List and PDB-Annotated at Brussels Free U., Belgium and PDB-Select at EMBL-Heidelberg W3
*1* PDB At A Glance - Hierarchic Access to PDB Files at NIH W3
*2* PDBFINDER - A Database Containing PDB, DSSP and HSSP Information (see Documentation) at EMBL-Heidelberg W3
*2* PDBSTR - Re-organized Protein Data Bank at GenomeNet, Japan W3
*2* PepPepSearch[E] - Search SwissProt for a Peptide Sequence at ETH-Zürich, Switzerland W3
dot Plant EST Analysis - Similarity Analysis of Different Plant cDNA/EST Sequences at U. Minnesota W3
*1* PHD[L][E] - Predict Protein Secondary Structure at EMBL-Heidelberg w/ search from Iowa State W3
*2* PHILIP-Bootstrapping Analysis - Divergence Between Protein or Nucleotide Sequences at Institut Pasteur, France W3
dot Phospepsort - Digest Phosphorylated Peptide Sequences at EERIE-Nimes, France W3
dot pI/Mw - Compute the Theoretical pI and Molecular Weight of a Protein Sequence at ExPASy, Switzerland W3
*1* PIR - Protein Identification Resource Database at Johns Hopkins W3
dot PIRALN - Database of Sequence Alignments based on PIR at EMBL-Heidelberg W3
dot PMD - Protein Mutant Database at GenomeNet, Japan and PMD at EMBL-Heidelberg W3
dot PMOTIF - Search Protein Motifs in Gene Sequence at U. Minnesota W3
dot Poland - Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA at Uni-Düsseldorf, Germany W3
*1* PredictProtein[E] - Predict Protein Secondary Structure at EMBL-Heidelberg W3
*1* PRF - Protein Research Foundation Sequence Database at GenomeNet, Japan W3
*2* Primer - Select PCR Primers in a Gene Sequence at WICGR-MIT and Primer at U. Minnesota W3
*2* PRINTS - Protein Motif Fingerprints Database (see Documentation) and PRINTS-ALIGN at UCL-London, UK and PRINTS at EMBnet-Basel, Switzerland W3
*1* ProDom - A Protein Domain Database and ProDom-Search at INRA-Toulouse, France, ProDom and ProDom-Search at Sanger Centre, UK and ProDom at EMBL-Heidelberg (W3)
dot ProfileScan - Search a Sequence Against a Library of Profiles at ISREC, Switzerland W3
*2* ProLink - Integrated Database of Protein Structure, Sequence Homology, and Functional Pattern Information at BMERC (Gopher)
*2* PROPSEARCH[E] - Protein Sequence Search for Structural Homology Based on Aminoacid Properties at EMBL-Heidelberg W3
*1* PROSITE - Protein Sites and Patterns Database at ExPASy, Switzerland, PrositeScan at ISREC, Switzerland and PROSITE-Search[E] at EMBL-Heidelberg W3
dot Protein-Extras at EMBL-Heidelberg FTP
dot Protein Families[L] - Links to Information on Different Protein Families at Iowa State W3
*2* Prot-ID - Identify a Protein from Masses of Enzymatic Digestion Peptide Fragments at Rockefeller U. W3
dot Protein Motions - DataBase of Protein Movements at Stanford U. W3
*2* PSA[E] - Protein Sequence Analysis for Sequences of Unknown Structure at BMERC/MBCRR W3
*1* PSORT - Predict Protein Sorting Signals Coded in Amino Acid Sequences at GenomeNet, Japan W3
*2* PSSP - Protein Secondary Structure Prediction at Baylor College of Medicine W3
*1* PUMA - Phylogeny of Unicellular Organims with Metabolism and Alignments from MCS-Computational Biology at Argonne National Laboratory W3
dot PUU - Protein Domains Database Based on PDB-Select at EMBL-Heidelberg FTP
dot RDP - Ribosomal Database Project at U. Illinois W3
*2* ReBase - Restriction Enzyme Database and ReBase-Search at New England Biolabs, ReBase at EMBL-Heidelberg and ReBase at Johns Hopkins W3
dot REPRO[E] - Recognition of Protein Sequence Repeats at EMBL-Heidelberg W3
dot RNA Secondary Structures - Information on Group I Introns and rRNA at U. Colorado-Boulder W3
dot rRNA - Databases of Ribosomal Subunit RNA Sequences at U. Antwerp, Belgium W3
dot RSVP - Rapid Sequence Visualization in Postscript for Analysis of DNA Sequences at CBIL-U. Pennsylvania W3
*2* SAPS - Statistical Analysis of Protein Sequences at ISREC, Switzerland W3
*2* SBASE - Library of Protein Domains and SBASE-Search [E] at ICGEB-Trieste, Italy W3
dot SCANPS - Scan Protein Sequences at U. Oxford, UK W3
*1* SCOP - Structural Classification of Proteins at Cambridge, UK and SCOP at U. South Florida W3
dot Sequence Annotation - Annotations on NCBI Sequences at Baylor College of Medicine W3
dot Sequence Translation - Translate Gene Sequences at U. Minnesota W3
dot Sleuth - Amino Acid Conformation and Solvent Accessibility of PDB Files at Washington U. FTP
dot SOPM[E] - Self Optimized Prediction Method for Prediction of Protein Secondary Structure at IBCP-CNRS, France W3
*1* SRSWWW - Network Browser for Databanks in Molecular Biology (w/ diagram links) at EMBL-Heidelberg W3
*1* SRSWWW-Directory - Directory of SRSWWW Network Browsers for Biological Databanks and SRSWWW-Global Status at EMBnet-Basel W3
*2* SSEARCH[E] - Universal Sequence Comparison Using the Smith-Waterman Algorithm at EERIE-Nimes, France W3
*2* SSPRED[E] - Predict the Secondary Structure of Proteins at EMBL-Heidelberg, Germany W3
*2* STRIDE - Find Secondary Structural Elements in PDB Proteins Structures at EMBL-Heidelberg W3
*2* STS Pipeline - Analysis and STS Primer Picking of Short DNA Sequences with Duplicate Checking, Sequence Repeat Finding, Restriction Analysis, Vector Identification and BLAST Searching at MIT W3
*2* SURVOL - Analysis of Protein Atomic Volumes at UCMB, Belgium W3
*2* Swiss-2DPage - Two-dimensional Polyacrylamide Gel Electrophoresis Database at ExPASy, Switzerland W3
*2* SWISSDOM - SwissProt Entries in a ProDom Map at EBI, UK W3
*2* Swiss-Model [E] - Automated Protein Modelling at ExPASy, Switzerland W3
*2* SWISSNEW - New SwissProt Sequences at EBI, UK W3
*1* SwissProt - Protein Sequence Database (+ Weekly Updates) at ExPASy, Switzerland W3
*2* Swiss-Shop [E] - Automated SwissProt and Prosite Information Queries at ExPASy, Switzerland W3
*2* TBASE - Transgenic/Targeted Mutation Database at Johns Hopkins W3
*1* TFASTA - Match a Protein Sequence Against All Six Frames of GenBank Sequences at EERIE-Nimes, France W3
dot TFD - Transcription Factor Database at NIH Gopher
*2* TFFACTOR and TFSITE - Transcription Factor Data at EMBL-Heidelberg W3
dot Tm - Oligonucleotide Melting Point Determination at U. Minnesota W3
*2* TMAP[E] - Identification of Transmembrane Segments on a Protein Sequence at EMBL-Heidelberg W3
dot TMBASE - Transmembrane Protein Database at U. Lausanne, Switzerland FTP
*2* TMpred - Prediction of Transmembrane Regions and Orientation in Protein Sequencs at ISREC, Switzerland W3
*2* Translate - Translate a Nucleotide Sequence to a Protein at ExPASy, Switzerland and Translate at EBI, UK W3
*2* TreeGen[E] - Tree Generation from Distance Data at ETH-Zürich, Switzerland W3
*2* TREMBL - Database of Translated Peptide Sequences of All CDS Features from EMBL Sequences at EMBL-Heidelberg W3
*2* VecBase - Cloning Vector Sequence CAOS/CAMM, The Netherlands W3
*2* Vector-DB - Cloning Vector Database at Queen's U.-Kensington, Canada W3 , VECTOR at BEN, Belgium W3 , Vector at Johns Hopkins and Vector-ig at IVR, Kyoto-U., Japan Gopher
dot VisAlign - The Alignment Color Viewer to Color 2 Aligned Amino Acid Sequences by Hydrophobicity at EBI, UK W3
dot VisProt - The Protein Colorer to Color Amino Acid Sequences by Hydrophobicity at EBI, UK W3
dot WebLogo - Sequence Logo Generation at Cambridge U., UK W3
*2* ZPRED - MultPredict Secondary Structure of Multiply Aligned Protein Sequences at Ludwig Institute for Cancer Research, UK W3

Pedro welcomes any comments or suggestions of changes to this Page!

Last Modified: 96/06/15