Molecular Modeling 


"You need the willingness to fail all the time. You have to generate many idea

 and then you have to work very hard only to discover that they don’t work. 

And you keep doing that over and over until you find one that does work.”

                                                                                                  Mr. Backus 

 "Computers are incredibly fast, accurate, and stupid; humans are incredibly
slow, inaccurate and brilliant; together they are powerful beyond imagination."
                                                                                                 Albert Einstein

Community

Chemweb 

CCL 

Links

Computational Chemistry Resources

Molecular Modeling Software List

Bookmarks

ScienceDirect
PubMed

Journals 

My Research

old work includes (temp_c++3, MULTIproteING)

collaboration ( ProtLib (docs) , ProtLib (source))

Research Centers

Europian Bioinformatics Institute
Computational Biology Research Center (Japan)
Computational Biology Service Unit (Cornell Theory Center)

Protein Folding People

Folding Groups
Folding Groups 2
Baker Lab (U of Washington)
Fleming Lab (John Hopkins)
Sali Lab (UCSF)
Andrzej Kolinski's Lab (Warsaw Univ., Poland)
Meller Group (Cincinnati Children's Hospital)
Jeffrey Skolnick (Georgia Tech)
Abrams' multiscale group for polymers
Roux Lab (U.Chicago)
Clote Lab
Karypis Lab

Protein Docking People

Docking sites

Ion Channels

Ion Channel Media
TransportDB

Protein Prediction Competitions

CASP Competition (runs every even year)
CASP7 targets
CASP6 targets
CASP5 targets
CAPRI: Critical Assessment of PRediction of Interactions

Protein Databases

Molecular Class-Specific Information System (including: GPCRDB, NucleaRDB, PrionDB, KChannelDB, GPCRIPDB)

Membrane Protein Database
The Protein Coil Library
DASSD (dihedral angle and secondary structure database)
Protein Ligand Databases
PDB (protein database)
Protein Classes

Protein Viewers

MolViZ.Org
Atlas of Protein Side-Chain Interactions
Lots of links to protein related research!!! Review on Free Molecular Graphics Software for Windows
List of Molecular 3D Modeling Programs

Servers (very big list)

Online Analysis Tools 

Molecular Biology Resorce 

DBAli (Sali)

PAPIA (retrieve PDB list by criteria)
UCLA-DOE Servers
Reconstruction of SC and BB from CA-trace
Amino Acid 1<-->3 letter code converter
Frequency count of amino acids in sequence
YASSPP (secondary structure prediction)

pKa Calculations (list)

H++ (protonation and pKa)
PDB2PQR file conversion
PROPKA (pKa values)

Other 

Expasy (2 sequence alignment)
Solvent accessible area from given pdb file
Hydropathicity Plots
Protein Information Resource
VEGA Converts PDB files in other formats and vice versa
Secondary structure prediction of proteins from a sequence
POPS Server (Calculates Accessible Surface Areas)
Gert Vriend
Go model builder
DLOOP (loop scoring function) 

Ion pathways

Caver 

HOLE 

VMD

VMD (case studies)

VMD (download) 

VMD (script library) 

MDtools