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.