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Protocols

MolMovDB specifications

Information


Unique identifier OMICS_21052
Name MolMovDB
Alternative name Database of Macromolecular Movements
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Mark Gerstein

Publications for Database of Macromolecular Movements

MolMovDB citations

 (16)
library_books

The evolution of function within the Nudix homology clan

2017
Proteins
PMCID: 5389931
PMID: 27936487
DOI: 10.1002/prot.25223

[…] 2008). CE, DaliLite, and MultiProt/STACCATO were run locally. Alignments generated via SSAP and Structal were run on their servers, accessed at http://www.cathdb.info/cgi-bin/SsapServer.pl and http://molmovdb.mbb.yale.edu/align/, respectively. We then manually combined the results from these programs to generate a structure‐guided sequence alignment for 46 PDB structures. The resulting sequence al […]

library_books

Origin and evolution of transporter substrate specificity within the NPF family

2017
eLife
PMCID: 5336358
PMID: 28257001
DOI: 10.7554/eLife.19466.033

[…] ating the conformational stability of the transporter structures.10.7554/eLife.19466.029Figure 9.To determine the intracellular cavity/channel we used 3V () via the web interface found at http://3vee.molmovdb.org.VMD () was used for visualizing and displaying homology models and cavity/channel. […]

library_books

AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1 Proteinase Inhibitor

2016
PLoS One
PMCID: 4805282
PMID: 27008547
DOI: 10.1371/journal.pone.0151902

[…] e the Shrake method was applied to calculate Van der Waals radii and to assess the solvent accessible surface area. Additionally, the volume was calculated with 3V (Voss Volume Voxelator: http://3vee.molmovdb.org) volume assessor by rolling a virtual probe over the 1qlp protein surface [,]. The probe radius of 1.4, 3 and 10 Å was applied to obtain the solvent-excluded volume and protein shell volu […]

library_books

The Role of Distant Mutations and Allosteric Regulation on LovD Active Site Dynamics

2014
Nat Chem Biol
PMCID: 4028369
PMID: 24727900
DOI: 10.1038/nchembio.1503

[…] to AMBER format using the VMD software and were analyzed using the AMBERTOOLS utilities (ptraj module). Solvent-accessible volumes of active site entrance channels were measured using 3V (http://3vee.molmovdb.org/). […]

call_split

Molecular, Immunological, and Biological Characterization of Tityus serrulatus Venom Hyaluronidase: New Insights into Its Role in Envenomation

2014
PLoS Negl Trop Dis
PMCID: 3923731
PMID: 24551256
DOI: 10.1371/journal.pntd.0002693
call_split See protocol

[…] ed proteins), into the modeling program. Models with the lowest folding energy were selected and analyzed with ProSA . The groove volume calculation was performed using the 3V web server (http://3vee.molmovdb.org) . Epitopes mapped by spot-synthesis were located and visualized in the 3D model with PyMol . […]

library_books

Classification of Domain Movements in Proteins Using Dynamic Contact Graphs

2013
PLoS One
PMCID: 3832408
PMID: 24260562
DOI: 10.1371/journal.pone.0081224

[…] proteins.In an influential review of protein domain movements using structures from the PDB, Gerstein et al. saw two main types: predominantly hinge and predominantly shear. Following this study the DataBase of Macromolecular Movements (DBMM) appeared online with further examples . A number of other large-scale studies have been made using structures from the PDB each approaching the problem from […]

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MolMovDB institution(s)
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
MolMovDB funding source(s)
Supported by the National Science Foundation (Grant DBI-9723182).

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