Hyperlinked Tables and PFAM models compared to experimental structures from Briefings in Bioinformatics 2020

Hyperlinked tables

Table 1. Webservers for template-less protein structure prediction. The list follows alphabetical order only.

Server [ref]	URL	Underlying methods	Assessment	Max. models delivered	Quality estimate	Output
C-QUARK [22]	https://zhanglab.ccmb.med.umich.edu/C-QUARK/	ML-assisted contact prediction	CASP13 [16]	5	Own C-score (QUARK-like) plus estimated TM score and RMSD	Models and contact map
C-I-TASSER [22]	https://zhanglab.ccmb.med.umich.edu/C-I-TASSER/	ML-assisted contact prediction	CASP13 [16]	5	Own C-score (I-TASSER-like) plus estimated TM score and RMSD	Models, predicted contact map, and extended I-TASSER-like analysis (PDB structural matches, gene ontology predictions, predicted ligands, etc.)
RaptorX-Contact [23]	http://raptorx.uchicago.edu/ContactMap/	Contact prediction	CASP13 [16]	5	Own score plus residue-wise score estimated from CNS restraint violations	Models and predicted contact map
RaptorX-DeepModeller [23,24]	http://raptorx.uchicago.edu/StructPredV2/predict/	Contact and distance prediction	CASP13 [16]	5	Own score plus residue-wise scores estimated from CNS restraint violations	Models and predicted contact and distance maps
Robetta [26–28]	https://robetta.bakerlab.org/	Rosetta assisted by contact predictions and homology modeling using PDB and the Gremlin/Rosetta dataset of Table 2	CASP13 [16]	5	Estimated GDTTS for global quality (linearly related to TM score), plus residue-wise quality estimates	Models, intermediate predictions, quality estimate plots
trRosetta [21]	https://yanglab.nankai.edu.cn/trRosetta/	Contact, distance and orientation prediction	Not available; presumably similar to AlphaFold [21]	5	Estimated TM score and RMSD	Models, predicted contacts, distances and orientations

Table 2. Databases of precomputed models. See overlap and PFAM coverage in Figure S3; and examples comparing predictions to subsequent structures in Figure S4. The list follows alphabetical order only.

Dataset [ref]	URL	Underlying methods	Quality estimate for models	Average TM score in our tests	Additional comments
DMPfold [32]	http://bioinf.cs.ucl.ac.uk/downloads/dmpfold/pfam_models.tgz	Contact predictions from DeepMetaPSICOV, associated server at http://bioinf.cs.ucl.ac.uk/psipred/	Estimated TM scores on Github site	0.54 (9 models)	Main table includes models expected of high quality, but website includes many more predictions: https://github.com/psipred/DMPfold
Gremlin/Rosetta, 2015 [30] and 2017 [26]	https://gremlin2.bakerlab.org/meta/aah4043_final.zip and https://gremlin2.bakerlab.org/struct.php	Rosetta assisted with contact predictions from Gremlin	Own scores	0.80 (12 models)	Website includes comparisons to actual structures, showing that most are not new folds: https://gremlin2.bakerlab.org/meta_struct.php
PConsC3 [31]	http://c3.pcons.net/static/download/pfam.tar.gz	PConsC3 server at http://c3.pcons.net/pred/	Own scores	0.51 (13 models)	See associated server for user submissions and additional data at http://c3.pcons.net/pred/
Tara3D [33]	https://zhanglab.ccmb.med.umich.edu/Tara-3D/	C-I-QUARK server from Table 1	Estimated TM scores on authors’ website	0.53 (9 models)	Used marine metagenomics. See https://zhanglab.ccmb.med.umich.edu/Tara-3D/
Modelsearch [34]	http://lucianoabriata.altervista.org/modelsearch/	(This website provides a sequence search interface for the datasets above plus others)

Table S2. Servers for pure contact prediction and coevolution calculations.

Service	URL	Reference
DCA (pure coevolution)	http://dca.rice.edu/portal/dca/dca-webservice	Morcos et al. PNAS 2011
DeepMetaPSICOV (contact prediction)	http://bioinf.cs.ucl.ac.uk/psipred/	Kandathil et al. Proteins 2019
EVCouplings (pure coevolution)	https://evcouplings.org/	Marks et al. Plos One 2011
Gremlin (pure coevolution)	http://gremlin.bakerlab.org/	Anishchenko et al. PNAS 2017

Table S3. Servers for modeling predicting contacts between pairs of proteins. Note this technology is less developed than normal contact predictions and results are far less reliable.

Service	URL	Reference
EVComplex	https://evcouplings.org/complex	Zeng et al. Nucleic Acids Res. 2018
Gremlin complex	http://gremlin.bakerlab.org/cplx_submit.php	Ovchinnikov et al. eLife 2014
RaptorX complex	http://raptorx.uchicago.edu/ComplexContact/	Hopf TA et al. eLife 2014

Download PFAM models and experimental structures from Figure S3

PFAMmodelsVSexpstruct.zip

Download PFAM models and experimental structures from Figure S3

Other related links