Learning protein and its structure | Database (gene, protein) & bioinformatics | Calculation | Journal & libraries | Experimental protocols | Scientific Societies | Crystallography laboratories | structural genomics | Science updates | Vendors | Fun
 

Learning protein and its structure

 
What is a Protein?
How Do Proteins Fold?
Beginner's Guide to Molecular Biology
Nature of 3-D Structural Data
Principles of Protein Structure
Introduction to Protein Structure
Biochemistry in 3-D: Lehninger Principles of Biochemistry
The Structures of Life
Nucleic Acid Structure and Recognition

Database (gene, protein) & bioinformatics

 
XtalPred Prediction of Protein Crystallizability
DisProt  Database of Protein Disorder
PDB Protein Data Bank
BMCD Biological Macromolecule Crystallization
CCDC: Cambridge Crystallographic Data Centre (small molecules)
Genestream Bioinformatics Resource Server
FSSP Sequence alignments of proteins with known 3D structures
EXPASY Proteomic Tools
Entrez NCBI databases
TIGR Institute for Genomic Research
EMBL
GENBANK
International Nucleotide Sequence Database Collaboration
SWISS-PROT and TrEMBL
PIR
CARB Bank Oligosaccharide structures
DisEMBL protein disorder prediction
GlobPlot predictor of protein disorder and globularity
K-JIST Group of Korean Structural Proteomics Research Organization prtein sequence analysis
Heavy Atom Derivative Database

Calculation

(Stability Prediction)
 
Eris: an automated estimator of protein stability
 
(Homogy modeling)
 
123D
ICM
JACKAL
MODBASE Database of protein structures obtained by homology modeling
SWISS-MODEL Web based tool for generating homology models
WHAT IF Web based tool for generating homology models
MODELLER
3DCrunch
 
(Threading)
 
THREADER2
PHDthreader
T3P2 UCLA threading
3D-PSSM
 
(docking, virtual screening)
 
AutoDock
Bielefeld Protein Docking
DOCK
DOT
FTDock, RPScore and MultiDock
GRAMM
Hex 3.0
ICM Protein-Protein docking
KORDO
MPI Protein Docking
Nussinov-Wolfson Structural Bioinformatics Group
 
(MD, MM calculation)
 
ANALYZE
AMBER
AutoDock3.0
CHARMM
ECEPPAK
GROMOS
GROMACS
ICM
JACKAL
MidasPlus
NAMD

Journal & libraries

 
PUBMED
HIGHWIRE
BIOMEDNET
SPRINGER
OXFOR JOURNALS
CRYSTALLOGRAPHY JOURNAL ONLINE:
Acta Crystallographica Section A: Foundations of Crystallography
Acta Crystallographica Section C: Crystal Structure Communications
Acta Crystallographica Section D: Biological Crystallography
Acta Crystallographica Section E: Structure Reports Online
ADVANCES IN ENZYME REGULATION
ADVANCES IN PROTEIN CHEMISTRY
ANALYTICAL BIOCHEMISTRY
ANNUAL REVIEW OF BIOCHEMISTRY
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
BIOCHEMICAL JOURNAL
BIOCHEMICAL PHARMACOLOGY
BIOCHEMISTRY
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
BIOCHIMICA ET BIOPHYSICA ACTA
Biochimica et Biophysica Acta – Bioenergetics
Biochimica et Biophysica Acta – Biomembranes
Biochimica et Biophysica Acta – Gene structure and expression
Biochimica et Biophysica Acta – General Subjects
Biochimica et Biophysica Acta-Molecular Basis Of Disease
Biochimica et Biophysica Acta- Proteins And Proteomics
Biochimica et Biophysica Acta-Reviews On Biomembranes
BIOINFORMATICS
BIOPHYSICAL JOURNAL
CELL
CELL BIOCHEMISTRY AND FUNCTION
CELL STRESS & CHAPERONES
CELLULAR AND MOLECULAR BIOLOGY
CELLULAR AND MOLECULAR LIFE SCIENCES
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
CURRENT BIOLOGY
CURRENT OPINION
Current Opinion In Biotechnology
Current Opinion In Cell Biology
Current Opinion In Structural Biology
EMBO Journal
EUROPEAN JOURNAL OF BIOCHEMISTRY
FASEB JOURNAL
FEBS LETTERS
GENE
GENES & DEVELOPMENT
GENE THERAPY
GENES TO CELLS
GENOME RESEARCH
GENOMICS
THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND CELL BIOLOGY
JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
JOURNAL OF BIOLOGICAL CHEMISTRY
JOURNAL OF BIOTECHNOLOGY
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
JOURNAL OF CELL BIOLOGY
JOURNAL OF CELLULAR BIOCHEMISTRY
JOURNAL OF GENE MEDICINE
JOURNAL OF MOLECULAR BIOLOGY
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC
JOURNAL OF MOLECULAR MODELING
JOURNAL OF MOLECULAR STRUCTURE
JOURNAL OF PROTEIN CHEMISTRY
JOURNAL OF STRUCTURAL BIOLOGY
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
MOLECULAR AND CELLULAR BIOCHEMISTRY
MOLECULAR AND CELLULAR BIOLOGY
MOLECULAR BIOLOGY OF THE CELL
MOLECULAR BIOTECHNOLOGY
MOLECULAR CELL
MOLECULES AND CELLS
MUTAGENESIS
MUTATION RESEARCH-DNA REPAIR
NATURE
NATURE BIOTECHNOLOGY
NATURE CELL BIOLOGY
NATURE GENETICS
NATURE STRUCTURAL BIOLOGY
NUCLEIC ACIDS RESEARCH
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICAN
PROTEIN ENGINEERING
PROTEIN EXPRESSION AND PURIFICATION
PROTEIN SCIENCE
PROTEINS-STRUCTURE FUNCTION AND GENETICS
SCIENCE
STRUCTURE WITH FOLDING & DESIGN
TRENDS IN BIOCHEMICAL SCIENCES
TRENDS IN BIOTECHNOLOGY
TRENDS IN CELL BIOLOGY

Experimental protocols

(biochemistry, molecular biology protocols)
 
Molecular biology protocols
Biochemistry protocols
Methods and protocols in biochemistry

Scientific Societies

 
International Union of Crystallography (IUCr)
American Crystallographic Association
British Crystallographic Association
German Crystallographic Association
Swiss Society for Crystallography
European Crystallographic Association
Korean Crystallographic Association
The Crystallographic Society of Japan
American Association for the Advancement of Science (AAAS)
The Association of Biomolecular Resource Facilities (ABRF)
American Society for Biochemistry and Molecular Biology (ASBMB)
Federation of European Biochemical Societies (FEBS)
Federation of American Societies for Experimental Biology (FASEB)
International Union of Biochemistry and Molecular Biology (IUBMB)
European Molecular Biology Organization (EMBO)
The Biochemical Society of the Republic of Korea (BSRK)
The American Society for Cell Biology (ASCB)
The Max-Planck Society
The Protein Society

Crystallography laboratories

 
Pamela Bjorkman Group, California Institute of Technology, US
Alex Brunger Group, Stanford University, US
Stephen Burley Group, Rockefeller University, US
Seth Darst Group, Rockefeller University, US
Johann Deisenhofer Group, University of Texas Southwestern Medical Center, US
Richard Ebright Group, Rutgers University, US
Soo Hyun Eom Group, Kwangju Institute of Science and Technology, Korea
Stephen Harrison Group, Harvard Medical School, US
Wayne Hendrickson Group, Columbia University, US
Wim Hol Group, University of Washington, US
Robert Huber Group, Max-Plank-Institute of Biochemistry, Germany
Fred Hughson Group, Princeton University, US
Sung-Hou Kim Group, University of California-Berkeley, US
John Kuriyan Group, University of California-Berkeley, US
Alex McPherson Group, University of California-Irvine, US
Hartmut Michel Group, Max-Plank-Institute of Biophysics, Germany
Byung-Ha Oh Group, POSTECH, Korea
Nicola Pavletich Group, Memorial Sloan-Kettering Cancer Center, US
David Richardson Group, Duke University, US
Timothy Richmond Group, Swiss Federal Institute of Technology (ETH), Switzerland
Yigong Shi Group, Princeton University, US
Frank Sicheri Group, University of Toronto, Canada
John Sondek Group, University of North Carolina-Chapel Hill, US
Stephen Sprang Group, University of Texas Southwestern Medical Center, US
Thomas Steiz Group, Yale University, US
Natalie Strynadka Group, University of British Columbia, Canada
Se Won Suh Group, Seoul National University, Korea
Ian Wilson Group, The Scripps Research Institute, US
Cynthia Wolberger Group, Johns Hopkins University School of Medicine, US
Hao Wu Group, Weill Medical College of Cornell University, US

Structural genomics

 
New York Structural Genomics Research Consortium, US
Midwest Center for Structural Genomics, US
Berkeley Structural Genomics Center, US
Structural Genomics at Brookhaven National Laboratory, US
Northeast Structural Genomics Consortium, US
Southeast Collaboratory for Structural Genomics, US
Joint Center for Structural Genomics, US
TB Structural Genomics Consortium, US
Proteomics Clinical Genomics Centre University Health Network, Canada
NIH Structural Genomics Initiatives, US
Protein Structure Factory, Germany
European Structural Genomics Consortium SPINE, Germany
Oxford Protein Production Facility, UK
RIKEN Structural Genomics Initiative, Japan

Science updates

(web sites containing useful biological information)
 
BRENDA The Comprehensive Enzyme Information System
The Cytokines Web
ENZYME Enzyme Nomenclature
GENECARDS Database on human genes, proteins and diseases
GPCRDB Information system for G protein-coupled receptors (GPCRs)
ImMunoGeneTics Database IMGT, nucleotide sequence information of genes important in the function of the immune system
MEROPS Peptide database
METALLOPROTEIN Database and Browser
OMIM Online Mendelian Inheritance in Man, this database is a catalog of human genes and genetic disorders
PROLYSIS Proteases and protease inhibitors
Protein Kinase Resource
RELIBase Structural data about receptor/ligand complexes
Structural Bioinformatics, Inc. (SBI) Databases of drug targets, structural polymorphisms, and comparative analysis of protein structures

Vendors

(drug, instrument, molecular biology reagent companies)
 
Amersham Bioscience
Beckman
BMS KOREA
Hampton Research
Intron
LG life science
Macrogen
MERCK
Millipore
Novagen
Promega
SIGMA-ALDRICH
SK Pharma
TaKaRa

fun

 
Internet hankyoreh
JoongAngllbo
Digital Chosunilbo
Hankookilbo
The KOREA TIMES
Newsweek
Weather news