Links
Links
Solvation
Minnesota Solvation Database experimental database for use with QC
FreeSolv experimental database for use with MD
VEASTA visualisation for electronic structural analysis, solid state
Pseudo Potentials, Basis Sets and Force Field parameters
link to a site that downloads basis sets and pseudopotentials in a number of different program formats
Force field parameter sets (from the Goodman group in Cambridge)
software from the Bonn groups such as xtb, dftd3, dftd4, TRAVIS, ORCA.
Molecular Visualization/Analysis
Database Searching by Sequence Similarity
Sequence Alignment
T-COFFEE - multiple sequence alignment
ClustalW @ EBI - multiple sequence alignment
SPEM - multiple sequence alignment
DiAlign - multiple sequence alignment
Structure Alignment
MatchMaker tool in Chimera - pairwise
FAST - pairwise; paper compares the method to DaliLite, CE, and K2
MultiProt - truly multiple rather than assembly of pairwise alignments
SuperPose - multiple
SALIGN - multiple
K2, K2SA - pairwise
CE (pairwise), CE-MC (multiple, building upon pairwise CE alignments)
DaliLite - pairwise
Protein3Dfit - pairwise
Protein 3D Structure Resources
PDB - protein 3D structure database
RasMol / Protein Explorer - molecule 3D structure viewers
SCOP - Structural Classification Of Proteins
FSSP - fold classification based on structure-structure alignment of proteins