Model deposition statistics from december 2018 until april 2019 (included)
Manual estimation of the fraction of models reported in literature that are made available online
Journal and Link
|
Protein(s)
|
Methods
|
Available? |
December 2018 (21 hits that actually report computational or integrative biomolecular models) |
|||
https://www.ncbi.nlm.nih.gov/pubmed/30733793
J Genet Eng Biotechnol |
Antifreeze proteins from Ocean pout |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30686667
Structure |
Ghrelin bound to its GPCR |
Integrative model from NMR, mutagenesis, experimental structures and comparative models |
Yes, at PDB-dev |
https://www.ncbi.nlm.nih.gov/pubmed/30586225
Chem Biol Drug Des |
Human Histamine H3 receptor |
Homology modeling |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30563894
mBio |
CcsBA Heme Exporter/Cyt c Synthetase |
ROSETTA with coevolution data |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30556504
Med Chem |
α-amylase from Anoxybacillus sp. |
Homology modeling and MD simulations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30555066
J Genet |
Human WNT10A |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30544954
Molecules |
AIM1 g1g2 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30414406
J Mol Biol |
Bc- TubR:S48eco complex |
SAXS data and MD simulation from assembled model |
Yes, at SASBDB |
https://www.ncbi.nlm.nih.gov/pubmed/30482862
Proc Natl Acad Sci U S A |
SNARE-based bilayers fusion pore |
Built from protein x-ray structures and model membranes, then subject to coarse-grained MD |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30520531
Proteins |
Extracellular portions of the THSD7A antigen |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30521151
FEBS J |
ABA-D6F10 Fv and ABA-Ribosome complexes |
Homology modeling and docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30527201
Kaohsiung J Med Sci |
Class III chitinase from corms of Gladiolus grandiflorus |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30373772
J Biol Chem |
Lysophospholipid transport K |
Homology modeling, and docking of lipids on models |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30412317
Ann Neurol |
human ColGalT1 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30290254
Int J Biol Macromol |
Carboxylesterase from Bacillus licheniformis |
Homology modeling, compared to SAXS data |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30278209
Microb Pathog |
Ergosterol enzyme of T. harzianum |
Homology modeling, MD, docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30121301
Int J Biol Macromol |
Ornithine/citrulline carrier |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30159640
Mol Biol Rep |
Arthrospira platensis Δ9 desaturase |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30251665
Biochim Biophys Acta Gen Subj |
CD28/B7-1 complex |
Docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30266731
Appl Environ Microbiol |
Fungal Polyphenol Oxidase |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30268755
Int J Biol Macromol |
Sortase A and related proteins from Enterococcus faecalis |
Homology modeling and docking |
No |
January 2019 (16 hits that actually report computational or integrative biomolecular models) |
|||
https://www.ncbi.nlm.nih.gov/pubmed/30721249
PLoS One |
ORP1-Rab7-RILP complex |
Combining structures of Rab7-RILP and ORP1 -Rab7 |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30706165
Parasitol Res |
Glyceraldehyde 3-phosphate dehydrogenase from Fasciola gigantica |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30700556
J Biol Chem |
First FNIII domain of mouse Robo2 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30682224
Epilepsia |
GNAO1 protein |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30679715
Sci rep |
Arabidopsis ATP-Binding Cassette Transporter AtABCC2 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30673861
J Mol Model |
DYRK1B protein kinase |
Comparative modeling and metadynamics simulations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30659061
Mol Cell Proteomics |
Apolipoprotein A1 dimer |
Built from PDB files and simulated in dynamics |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30638370
ACS Chem Neurosci |
γ-Secretase Aβ n Complex |
MD simulations from PDB structures |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30630949
J Biol Chem
|
Cytosolic complex of phagocyte NADPH oxidase |
Integrative model from partial structures, FRET and SAXS data |
Yes (partially), at SASBDB |
https://www.ncbi.nlm.nih.gov/pubmed/30626736
J Biol Chem |
Respiratory syncytial virus N0-P complex |
SAXS data |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30621365
Int J Mol Sci |
Novel Xylose Reductase |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30610890
Neurosci Lett |
hnRNP from squid brain |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30472604
Eur J Med Chem |
Adenylyl cyclase 1 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30384046
Eur J Med Chem |
Human P-glycoprotein |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/29241413
J Biomol Struct Dyn |
GidB from Mycobacterium tuberculosis |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30348830
J Bacteriol |
Histidine ATP-binding cassette (ABC) transporter of Salmonella enterica |
Homology modeling |
No |
February 2019 (14 hits that actually report computational or integrative biomolecular models) |
|||
https://www.ncbi.nlm.nih.gov/pubmed/30783168
Sci Rep |
Wsp.Man26A from Westerdykella sp |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30782848
J Biol Chem |
A. thaliana LYSOPL2 and docked poses |
Homology modeling and docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30774960
Pharmacol Res Perspect |
Gq-coupled receptor 139 and docked poses |
Homology modeling, docking and simulations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30784161
Diabetes Obes Metab |
Glucose-dependent insulinotropic polypeptide |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30791488
Int J Mol Sci |
S. lycopersicum vacuolar CAT2 Arginine Transporter |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30799091
Int J Med Microbiol |
Streptococcus dysgalactiae BrpA |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30765752
Sci Rep |
Jug r 3-Oleate complex |
Homology modeling, NMR-based docking, and simulation |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30769268
Comput Biol Chem |
COX1 and NAD1 from E. granulosus and E. canadensis |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30672911
Chem Commun |
HhC (HINT-SRR) bound to cholesterol |
Homology modeling, simulation |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30715856
Biochemistry |
S. enterica STM2437 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30718375
J Gen Physiol |
Alanine serine cysteine transporter 2 |
Homology modeling |
Paper not accessible |
https://www.ncbi.nlm.nih.gov/pubmed/30723160
J Biol Chem |
T1R2-T1R3 dimer |
Homology modeling, manual building considering mutagenesis data, and simulation |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30718375
J Gen Physiol |
H. sapiens type I collagen |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30462348
Chemistry |
Tetrameric ANSII |
Data-driven docking |
No |
March 2019 (20 hits that actually report computational or integrative biomolecular models) |
|||
https://www.ncbi.nlm.nih.gov/pubmed/30954210
Biophys J |
Light-Harvesting Complex II oligomers |
MD simulations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30929948
Bioorg Med Chem |
P. vivax M18 aspartyl amino peptidase |
Homology modeling, docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30879307
J Chem Inf Model |
Activated Human MEK1 |
Homology Modeling, docking |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30919327
Mol Biotechnol |
Mini Protein Design of Haloalkane Dehalogenase |
Homology modeling, docking, MD simulation |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30889428
J Mol Graph Model |
Gonadotropin releasing hormone receptor I |
MD simulation |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30891873
Pest Manag Sci |
P. capsici Cellulose synthase 3 |
Homology modeling, docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30898047
J Biomol Struct Dyn |
M. tuberculosis Rv1273c |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30862948
Sci Rep |
CD36-like protein |
Homology modeling and docking |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30877278
Eur J Hum Genet |
Human DPH1-DPH2 heterodimer |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30880082
J Struct Biol |
PAM dimer |
Ideal geometries |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30869893
J Med Chem |
Human Adenosine A3 Receptor |
Homology modeling |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30880628
J Biomol Struct Dyn |
Eukaryotic elongation factor-2 kinase |
Homology modeling, docking, simulations |
Paper unavailable |
https://www.ncbi.nlm.nih.gov/pubmed/30883570
PLoS One |
T1R3 subunit of human sweet taste receptor |
Docking and MD simulations |
Yes, in S.I. |
https://www.ncbi.nlm.nih.gov/pubmed/30715856
Biochemistry |
STM2437 |
Homology Modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30723160
J Biol Chem |
T1R2-T1R3 dimer of sweet taste receptor |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/29502488
J Biomol Struct Dyn |
α-subunit of M. tuberculosis tryptophan synthase |
Homology modeling, docking and simulations |
Paper unavailable |
https://www.ncbi.nlm.nih.gov/pubmed/30550846
Microb Pathog |
Undecaprenyl-diphosphatase |
Homology modeling and docking |
Yes, at Protein Model DataBase |
https://www.ncbi.nlm.nih.gov/pubmed/30610890
Neurosci Lett |
hnRNP type A/B protein from squid brain |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30664899
Biochimie |
S. mansoni dihydroorotate dehydrogenase |
Docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30682224
Epilepsia |
GNAO1 |
Homology modeling and docking |
No |
April 2019 (15 hits that actually report computational or integrative biomolecular models) |
|||
https://www.ncbi.nlm.nih.gov/pubmed/31024490
Front Microbiol |
PB2SF |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/31017232
Braz J Biol |
CXC chemokine receptor type 1 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30973886
PLoS One |
Pseudocerastes Persicus Trypsin Inhibitor |
Homology modeling and Brownian dynamics |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30976111
Eur J Hum Genet |
DHR-2 domain of human DOCK3 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30990934
Mol Microbiol |
Extracytoplasmic factors ECF41 and ECF42 |
Homology modeling and direct-coupling analysis |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30990952
Chem Biodivers |
ATP synthase |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30940649
J Biol Chem |
M013 pyrin domain |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30963603
Hepatology |
Glypican-3 |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30969795
FASEB J |
Kv1.3-KCNE4 complex |
Homology modeling and manual operations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30913878
J Phys Chem B |
Lysozyme Folding Intermediate |
Molecular simulations |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30921517
J Phys Chem B |
Cystic Fibrosis Transmembrane Conductance Regulator |
Optimization of previous CryoEM structure through Molecular Dynamics Flexible Fitting |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30342100
Biochim Biophys Acta Mol Cell Biol Lipids |
P. oxalicum 6R,8R-linoleate diol synthase |
Homology modeling and docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30387171
J Cell Biochem |
Purβ homodimer |
Homology modeling |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30618329
Biosci Biotechnol Biochem |
Antibody |
Homology modeling and docking |
No |
https://www.ncbi.nlm.nih.gov/pubmed/30769268
Comput Biol Chem |
Respiratory complexes |
Homology modeling |
No |
Notes
1) Search was:
protein and AND ("protein model" OR "homology model" OR "structural model") AND (("2019/01/01"[PDat] : "2019/01/31"[PDat])) (or corresponding date range)
2) Not listed above: Cases where the model was actually an NMR, x-ray or cryoEM structure and as such was available at the PDB; cases where the model was only a sketch representation; and a few cases that did not report any kind of structure or model at all.