Home | Timothy A. Springer CV | Research Projects | Springer Publications | Springer Career Narrative | Lab Members | Lab Protocols | Structure Gallery | Lab Goodies | Links | Positions Available
Harvard and IDI | Core Facilities | Databases | Prediction Servers | Software |
Other Bioinformatics Resources | Molecular Biology, Biochemistry, and Immunology |
Structural Biology | Courses | Journals | Catalogs | Other Labs and Organizations | Office Links
|
|||
| eCommons of Harvard Medical School Electronic journals, books, online databases, educational programs, and HMS institutes Online Safety Training Programs |
The CBR
Institute for Biomedical Research Harvard University White Pages of Harvard Medical School |
||
|
|||
| Research Computing Center at Harvard Medical School HMS Core Facilities Electron microscope, DNA sequencing, oligonucleotide synthesis, peptide synthesis, mass spectroscopy, amino acid analysis, machine shop, and confocal microscope Research Facilities at Department of Cell Biology light microscopy, conventional electron microscopy, molecular electron microscopy, bioinformatics, digital graphics, shared equipment, mass spectrometry, machine shop |
DFCI
Core Facilities AIDS drug screening, bioinformatics, biostatistics/consulting, cell manipulation and gene transfer, flow cytometry, hybridoma, in situ hybridization, medical arts, DNA sequencing, DNA and peptide synthesis, protein sequencing, BIAcore protein ligand assays, mass spectrometry, and molecular diagnostics. CBR Core Facilities calcium imaging system, cell sorter/flow cytometer, transgenic facility, multi-photon microscopy, C. elegans imaging system, and SKY system. Harvard Institute of Proteomics |
||
|
|||
| PubMed and Entrez search literature, Protein, Nucleotide, Genome, PopSet, OMIM, Taxonomy, Books, ProbeSet, and 3D Domains. Protein Data Bank (PDB) biomolecular structure database; SearchFields; links to macromolecular structure related resources; and more SCOP structural classification of proteins by class, fold, superfamily, family, protein, and species CATH a hierarchical domain classification of protein structures by class, architecture, topology (fold family), and homologous superfamily Dali server a network service for comparing protein structures in 3D ExPaSy (Expert Protein Analysis System) analysis of protein sequences, structures, and 2D PAGE; links to databases, proteomics tools and software packages, molecular biology resources, and more GenomeNet a Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology; DBGET/LinkDB - integrated database retrieval system; search >20 databases and >40 organisms The Genome Database (GDB) regions of the human genome, maps of the human genome, variations within the human genome Human Gene Mutation Database (HGMD) The Institute for Genomic Research (TIGR) comprehensive microbial resources, genomes of microbial, rice, parasites, virus, and more |
Homstrad: Homologous Structure Alignment Database access by browsing families, keyword search, blast search, and FUGUE search SMART: Simple Modular Architecture Research Tool sequence analysis; architecture analysis; domain searching and browsing; HMMs; and more Pfam: Protein families databases of alignments and HMMs a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains ProDom: The Protein Domain Database automatic compilation of homologous domains; analyze domain arrangements of proteins and protein families PROSITE: Database of Protein Families and Domains sites, patterns and profiles; various access and search tools; documentations; and more Blocks WWW Server compare a protein or DNA sequence to a database of protein blocks, retrieve blocks, create new blocks, and more PRINTS: Protein Fingerprint Database a fingerprint is a group of conserved motifs used to characterise a protein family; various access and search tools; documentation; and more eMOTIF eMOTIF Maker; eMOTIF search; eMOTIF scan; 3MOTIF The MEME System (Multiple EM for Motif Elicitation) discover motifs in groups of related DNA or protein sequences Cytokine Family Database (dbCFC) and Cytokine Receptor Family Database (dbCRF) collection of EST (Expressed Sequence Tag) records of cytokines and cytokine receptors deposited in the NCBI GenBank; related links to Cytokines Web, Chemokine Information Source, GPCRDB and GCRDb, and more |
||
|
|||
| Meta Server Job List A metaserver that accesses the most sensitive sequence similarity, secondary structure, and fold prediction servers, and provides a consensus jury prediction. 3D-PSSM Protein Fold Recognition Server |
Blast Search Bork Group's advanced WU-BLAST2 Search with post-processing at EMBL Tools at NIMR Protein tertiary structure prediction (DRAGON); Design and engineering of humanised mAbs (Humanisation by Design); Multiple alignment viewer (Mview); Finding repeats in protein sequences (REPRO); Structural Alignment of Proteins (SAP); Finding knots in protein structures (TOPOL) CBS prediction servers nucleotide and amino acid sequence analysis; predictions of promotors, intron splice sites, O-glycosylation sites (DictyOGlyc and NetOGlyc), phosphorylation sites, signal peptide (SignalP), transmembrane helices (TMHMM), and more Network Protein Sequence Analysis sequence similarity search; sites and signatures detection; multiple sequence alignment; secondary structure prediction with multiple methods; primary structure analysis such as physico-chemical profiles, coil-coiled detection, sequence coloring, and more Washington University in St. Louis Educational and Scientific Resource links in the field of Computational Biology PSIPRED The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via E-mail. You may select one of three prediction methods to apply to your sequence: PSIPRED - a highly accurate secondary structure prediction method, MEMSAT - our widely used transmembrane topology prediction method and GenTHREADER - a new sequence profile based fold recognition method. |
||
|
|||
| GeneMine/Look a sequence analysis and visualization program that makes full use of analysis servers across the Internet [Manual (PDF)] Lasergene by DNASTAR sequence analysis system for Windows and Macintosh; FAQ; Upgrades, Documents, and Library Rasmol and Chime Rasmol is free software for looking at molecular structures; Chime shows molecules inside a web page [Rasmol Manual and Chime Manual] Ribbons display, manipulate, and analyze molecular structures and produce high quality images in a variety of styles [Manual] MolMol a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules [Manual] GRASP a molecular visualization and analysis program; particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties [Manual] Modeller a program for homology protein structure modelling by satisfaction of spatial restraints [Manual] 3D Modeling Homepage at EMBL WhatIf a protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. [Manual: see the bottom of the home page] |
Barton Group Software Manuals for STAMP (Structural Alignment of Multiple Proteins), ALSCRIPT (Sequence alignment to PostScript), and DOMAK (DOMain Maker) JOY a program to annotate protein sequence alignment with structural features such as secondary structure, solvent accessibility, and hydrogen bonds [HOWTOs for JOY5 and Manual for earlier version] HMMER Profile hidden Markov models for biological sequence analysis [Manual] SAM (Sequence Alignment and Modeling system) a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis [Manual] GCG nucleic acid and protein sequence analysis [Manual (requires user ID and password)] Wise2 a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence [Manual] Phylip a package of programs for inferring phylogenies [Manual] Software at The Sanger Center production sequencing software, physical mapping software, informatics analysis software, format specifications Crystallography-related Software: ARP/wARP | CCP4 | CNS | Denzo/HKL | O | SHARP | SOLVE | Twinning Server | Uppsala Software Factory Unix Help Guide Local SGI Help |
||
|
|||
| The Bioinformatics Resource - CCP11 Project listings of bioinformatics training courses, glossaries, degree programs, jobs, research centers and groups, integrated databases, resources, and more EBI (European Bioinformatics Institute) database searching, browsing and analysis tools; Swiss-Prot + TrEMBL - annotated protein sequence database and computer-annotated supplement to SWISS-PROT (ExPaSy interface) Computational Services at EMBL sequence search, retrieval, and alignment; structure prediction and verification; and more BCM (Baylor College of Medicine) Search Launcher search nucleic acid sequences, gene features, protein sequences, protein patterns; multiple or pairwise sequence alignment; protein secondary structure prediction; BCM Gene Finder; BCM Human Transcript Database; and more |
Topical Net CUBIC Bioinformatics Links links to WWW introductions, search engines, general molecular biology sites, literature, pathways, genomes, databases, services, software, and companies; provided by Columbia University Bioinformatics Center Biology WorkBench search protein and nucleic acid sequence databases; integrated with analysis and modeling tools BIOCCELERATOR server at the Weizmann Institute of Science accelerated homology searches in sequence databases via GenWeb interface and using GenCore software; genomic analysis applications, including GenHunt and RepEater Pole Bio-Informatique Lyonnais at Institute of Biology and Chemistry of Proteins in France sequence database access; similarity searches; protein and DNA sequence analysis; and more |
||
|
|||
| CMS Molecular Biology Resource a compendium of tools and resources for molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling Molecular Biology Jump Station links to molecular biology sites and directories, protocols, journals, books, newsgroups and mail lists, genomes and databases, commercial sites, functional genomics, and more; provided by Molecular Biology Today Biology Links A-Z links to biochemistry and molecular biology, biomolecular and biochemical databases, educational resources, evolution, immunology, jobs, online journals, general internet bio-resources, and more; provided by Dept. of Molecular and Cellular Biology at Harvard University Bio Netbook a directory of Web pages for Biology; search by word, resource type, organism, biological domain, country, or combined Graphics Gallery of Biotechnology labeled diagrams with explanations representing the important processes of biotechnology; provided by Access Excellence at the National Health Museum |
Protein Review On The Web (PROW) PROW Guides, authoritative short, structured reviews on proteins and protein families. The Guides provide approximately 20 standardized categories of information (abstract, biochemical function, ligands, references, etc.) for each protein. Inflammation: The Leukocyte Adhesion Cascade The mechanisms, processes, cells, and molecules involved in inflammation; provided by Klaus Key at University of Virginia Therapeutic Immunology Group (TIG) monoclonal antibody info: research labs, articles, and protocols HLDA home page HDLA database; information on mAbs, cells, and CD names NWFSC Molecular Biology Protocols protocols, discussion forum, links to bioinformatics resources, journals, and more; provided by Northwest Fisheries Science Center at Seattle Sucrose Gradients vs. Gel Filtration estimate molecular size, shape, and Stokes radius using gel filtration and sucrose gradients |
||
|
|||
| Biological Macromolecule Crystallization Database (BMCD) crystal data and the crystallization conditions of >3000 crystal entries and >2000 biomolecules; NASA protein crystal growth archieve; references on crystallization; and more Database of Macromolecular Movements molecular motion classifications and movies Heavy Atom Databank Protein Structure Initiative (PSI) Structural Genomics Project at NIH Automation of Structure Determination Platform (ASDP) structural genomics centers and crystallography-related programs, databases, websites, libraries, tutorials, and bulletin boards archives |
CIMR Structural Medicine in University of Cambridge crystallography course, serpin database, crystallization page, and links TechCenter at Hampton Research (Solution for Crystal Growth): crystal growth 101, crystallization tips A to Z, tips and tricks, resources, product instructions, etc. Georgia X-ray Crystallography Center links to crystallography journals, databases, software, synchrotron sources, supplies, and more International Union of Crystallography (IUCr) American Crystallographic Association (ACA) |
||
|
|||
| Structure and Function of Proteins and Nucleic Acids offered by Stephen Harrison at Harvard University Protein Architecture, Dynamics and Structure Prediction offered by Michael Levitt at Stanford University Representations and Algorithms for Computational Molecular Biology offered by Russ Altman at Stanford University Computational Molecular Biology offered by Doug Brutlag at Stanford University |
Biological and Biomedical Sciences (BBS) Program and Immunology Program offered by the Division of Medical Sciences in Harvard Medical School Courses at Harvard University Courses at Harvard Extension School The Virtual School of Molecular Sciences courses in Structure-Based Drug Design, Java for Scientists, Bioinformatics Tools, Information Components using Java and XML |
||
|
|||
| Countway Library Electronic Journals access varies by title; Harvard ID required Science Citation Index Expanded find articles and citations by topic, person, or place; Harvard ID required Nature online archives beginning Jun., 1997 Science online archives beginning Oct., 1995 Cell Full text and summaries beginning Jan., 1996; summaries beginning May, 1974 |
Current Opinions in ... online archives beginning 1994; via BioMedNet PNAS online archives beginning Jan., 1990 EMBO J. online archives beginning Jan., 1984 JBC online archives beginning Jan., 1980 JMB online archives beginning Jan., 1996 Scientific American online archives beginning Jan., 1996 |
||
|
|||
| SciQuest the internet source for scientific products BioSupplyNet biomedical research supply information source |
ATCC | BioRad | Calbiochem | Hampton Research | Life Technology | New England BioLabs | Novagen | Amersham Pharmacia Biotech | Promega | Qiagen | Stratagene Computer Products at Harvard University Information Systems |
||
|
|||
| Peer Bork's Group BioInformatics Unit, Max Delbrück Center for Molecular Medicine, Berlin, Germany Chris Ponting MRC Functional Genetics Unit, Univerisity of Oxford, Oxford, UK George M. Church Lab WWW Server Department of Genetics, Harvard Medical School, Boston, USA Harrison/Wiley Laboratory Dept. of Molecular and Cellular Biology, Harvard University, Cambridge, USA |
Richardson Lab at Duke University GrantsNet funding opportunities for training in the biological and medical sciences National Institutes of Health The National Academies Laboratory of Molecular Biology, Medical Research Council (Cambridge, UK) European Molecular Biology Laboratory (Heidelberg, Germany) |
||