MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
Davis
Ian W
IW
Department of Biochemistry, Duke University, Durham, NC, USA.
Leaver-Fay
Andrew
A
Chen
Vincent B
VB
Block
Jeremy N
JN
Kapral
Gary J
GJ
Wang
Xueyi
X
Murray
Laura W
LW
Arendall
W Bryan
WB
Snoeyink
Jack
J
Richardson
Jane S
JS
Richardson
David C
DC
D019295:Computational Biology / Q000379:methods*; D006860:Hydrogen Bonding; D020407:Internet; D046911:Macromolecular Substances; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
D046911:Macromolecular Substances; D009696:Nucleic Acids; D011506:Proteins