| Group Name | Group Number | Pure FR | Alter method? | SS prediction | manual intervention | homologues | domain identification | fragment-based approach | use other servers | lattice-based | threading-like potentials | relaxation/ optimization/ minimization | other information |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SAM-T02-human | 001 | N. Not exclusively FR, although a FR step was always part of the process. | N | Y. Four neural nets trained on STRIDE, DSSP, STR, ALPHA11 | Y. Extensive manual intervention on the harder targets, assembling parts of the model by hand. Inspecting models, modifying cost function, re-optimizing, choosing models. | Y. MSA for predicting secondary structure and building an HMM, which is then used for fold recognition and generating fragments. | N. Generally started with whole chain, but sometimes broke this up into smaller pieces (not necessarily domains, as they sometimes overlapped) to repeat the fold recognition. | Y. Three fragment sources: generic, specific and long-fragment libraries. | Y. Used CAFASP output to confirm template selection; sometimes included Robetta models as possible conformations to modify in optimization process. | N | Y. Not a traditional pair-wise function, but a cost function based mostly on local environmental properties. Does not include hydrogen-bonding term, but does contain pairwise terms for cysteine residues. | N | - |
| BAKER | 002 | N | Y. Predictions were ab initio modelled, or modelled in the context of a template, depending on PCons2 score. | Y. PSIPred, Jufo, PHD | Y. Domain parsing, model selection. | Y. Secondary structure prediction, homologues predicted then clustered. | Y. Ginzu (in-house) | Y. Standard Rosetta library. | Y. Pcons to screen targets. | N | Y. Knowledge-based potential, physically based potential. | Y. Monte Carlo minimization; side-chains repacked using MC search through Dunbrack's rotamer library. | - |
| Skolnick-Kolinski | 010 | N. Uses FR to generate predicted contacts, but these need not come from proteins with the same global fold. | N | Y. PSIPred | N | Y. Multiple sequence alignments used to build profiles for threading-based contact prediction. Pair potentials averaged over homologues. | N. Domains were only identified if more than one template was found during the threading stage. | N | N | Y | Y. Pair, burial, secondary structure prediction. | Y. Assembly using replica exchange Monte Carlo. | - |
| ORNL-PROSPECT | 012 | Y | N | Y. PROSPECT-SSP (in-house program) | Y. Adjustments to minimize the number of long gaps and achieve better structural quality scores, assessed by WhatIf. | Y. Profile-profile alignment. | Y. Prodom | N | N | N | Y. Environment-specific (singleton) and pair contact potentials. | N | This is the manual version of group 195 (ORNL-PROSPECT server). |
| S:BAKER-ROBETTA | 029 | N | Y. Predictions were ab initio modelled, or modelled in the context of a template, depending on PCons2 score. | Y. PSIPred, SAM-T99, JUFO. | N | Y. Structures generated for family members then clustered; largest composite clusters submitted as predictions. | Y. Ginzu (in-house) | Y. Standard Rosetta library. | Y. Pcons to find ab initio targets. | N | Y. Environment and residue pair potentials. | N. Robetta uses only a low resolution centroid based representation of sidechains and a straight Monte Carlo search strategy. | - |
| S:Pmodel | 040 | Y | N | Y. PSIPred | N | N | N | N | Y. Consensus of mGenThreader, FFAS, Inbgu, 3D-PSSM, PDB-BLAST, SAM-T99, FUGUE. | N | N | N | - |
| S:Pmodel3 | 045 | Y | N | Y. PSIPred | N | N | N | N | Y. Consensus of INBGU-SHGU, FUGUE-2.1, ORFeus. | N | N | N | - |
| SAMUDRALA-NEWFOLD | 051 | N | N | Y. PSIPred | N. Method is completely automated. | N | Y. Domains were defined based on the number of secondary structure elements (in-house algorithm). | Y. About 30% of moves came from a 3-residue fragments of identical sequence. | N | N | Y. All-atom residue-specific conditional probability scoring function (similar to potential of mean force used by Sippl). | Y. ENCAD was used to eliminate any atom-atom overlaps and fix minor steric problems. | Same method as used by group 140. |
| Jones-NewFold | 068 | N | N | Y. PSIPred | N | Y. Energies are averaged over a set of aligned homologous sequences (created using PSI-BLAST). | N. Apart from removing domains with obvious sequence similarities. | Y. Library of super-secondary motifs and 3-5 residue fragments extracted from 200 high-resolution structures. | N | N | Y. THREADER3 potentials: beta-carbon distance-based potentials of mean force. | N | - |
| Friesner | 112 | N. A combination of fold recognition and simulation methods were used, depending on the target. | Y. Different methods were used for alpha-helical and mixed alpha-beta proteins. | Y. All secondary structure prediction methods used. | Y. Visual inspection of models. | Y. Multiple sequence information used to contruct profiles in threading. | Y. In some cases identified likely domains from secondary structure prediction. | N | N | N | Y. Statistical size-dependent potential. | Y. Simulations involved Monte Carlo moves followed by minimization. | - |
| S:I-Sites/Bystroff | 132 | N | Y. If the target has a PSI-BLAST hit, the alignment is used to assign coordinates. | Y. HMMSTR. | N | Y. PSI-BLAST. | N. Although sequences were split into overlapping domain-sized segments. | Y. I-sites library. | N | N | N | Y. Rosetta minimizes the energy during the simulation. | |
| S:PROTINFO-AB | 140 | N | N | Y. PSIPred | N | N | Y. Domains were defined based on the number of secondary structure elements (in-house algorithm). | Y. About 30% of moves came from a 3-residue fragments of identical sequence. | N | N | Y. All-atom residue-specific conditional probability scoring function (similar to potential of mean force used by Sippl). | Y. ENCAD was used to eliminate any atom-atom overlaps and fix minor steric problems. | Same method as used by group 051. |
| FAMS | 168 | Y | N | Y. PSIPred | N | N | N | N | N | N | N | Y. Simulated annealing process using homology modelling software, FAMS. | - |
| ORNL-PROSPECT | 195 | Y | N | Y. PROSPECT-SSP (in-house program) | N | Y. Profile-profile alignment. | N | N | N | N | Y. Environment-specific (singleton) and pair contact potentials. | N | This is the automatic server. Group 012 combines the server with manual intervention. |
| Pushchino | 203 | N | N | Y. Mainly PSIPred, but also Jpred, ALB (in-house). | Y. Visual inspection of alignments and/or models. | Y. Sequence and secondary structure profile used in threading. | Y. Identified domains using PSI-BLAST, HMMer and an in-house method. | N. Sometimes visual inspection led to good predictions of fragments being merged into a joint model. | N | N | Y. SCF_THREADER uses empirical potentials of short-range interactions | N | - |
| 3D-PSSM | 229 | Y | N | Y. PSIPred | N. Fully automated server. | Y. Template sequences aligned to PSI-BLAST target sequence profile. | N | N | N | N | Y. Jones' THREADER solvation potential. | N | - |
| Head-Gordon | 271 | N | N | Y. PSIPred | Y. Visual inspection during global optimization. | N | N | N | Y. Used CAFASP summaries to screen out easy FR and CM targets. | N | N. Physical all atom force field (AMBER) and hydrophobic solvation term derived in-house. | Y. Method focusses exclusively on local/global optimization. | - |
| Wolynes-Schulten | 294 | N | N | Y. Jpred and also a consensus based on PSIpred, PHD, Jpred, SSPro, and Prof. | Y. Visual inspection of top-scoring structures. | Y | Y. Variety of methods used: a search for exon/intron boundaries, examination of multiple sequence profiles, and results from the PRODOM and CAFASP servers. | N | Y. CAFASP used to screen targets. | N | Y. Associative memory terms combined with optimized contact potential and conventional threading potential (which contains pair, hydrogen bond, and profile potentials with a position dependent gap penalty). | Y. Energy function minimized using molecular dynamics with simulated annealing. | - |
| Scheraga-Harold | 314 | N | N | Y. Jnet, Jpred | Y. In most cases, final structures were selected by visual inspection. | N | Y. In some cases, domain definitions were based on CAFASP results. | N | Y. CAFASP results were used to detect domains. | N | N. Used a physics-based energy function (UNRES) with long-range and short-range energy components (including correlation terms). | Y. Conformational space annealing; energy minimization. | - |
| Shortle | 349 | N | N | Y. PSIPred, in-house method. | Y. Extensive visual creation/inspection of models. | Y. Used homologoues in secondary structure prediction and threading to find fragments. | N. Although sequences were often subdivided, with dividing lines between segments at high turn propensity and low hydrophobicity. | Y. Dunbrack's culled PDB set. | Y. PSI-BLAST was used to remove comparative modelling targets. Looked at output of some CAFASP secondary structure servers. | N | Y. Lawrence & Bryant's empirical pair potentials and in-house phi/psi/rotamer propensities and beta-carbon burial propensities | N | - |
| Brooks | 373 | N. Templates were used in cases where alignments were sufficiently good to allow the construction of reasonable (partial) 3D skeletons in agreement with secondary structure predictions. | Y. Ab initio was used whenever sufficient template information was not available. | Y. Consensus of PSIPred, PHD, SAM-T99, SSpro, as a bias for conformational searching. | Y. Visual inspection to select initial templates, manual docking of domains in some cases. | N | Y. In some cases, domains sampled separately then combined to a single structure. Domain boundaries identified based on alignment with different templates at different parts of the sequence. | N | Y. CAFASP servers were used to find templates. | Y. Ranking and refinement of structures was done using all-atom continuous-space models. | N | Y. All-atom force-field minimization and molecular dynamics for ranking and refinement. | - |
| Doniach | 401 | N | N | Y. PSIPred | Y. Picking and ranking submissions. | N | Y. PSI-BLAST | N | Y. GenTHREADER used to screen targets. | N | N | N | - |
| TOME | 450 | Y | N | Y. Predictions from JPred2 and those included in 3D-PSSM, mGenTHREADER or SAM-T99. | Y. Choice of template. | Y. Multiple sequence alignments re-threaded onto template to assess structural alignments. | Y. Domains sometimes assigned after initial threading runs identified regions corresponding to templates shorted than the target. | N | Y. Metaserver uses BLAST, 3D-PSSM, mGenTHREADER, FUGUE, SAM-T99 and JPred2. | N | Y. Pair potential derived from PKB (sidechain/sidechain interactions only). | N. Only when the model was built using MODELLER. | Main difference between this group and group 464 is choice of template. |
| ATOME | 464 | Y | N | Y. Predictions from JPred2 and those included in 3D-PSSM, mGenTHREADER or SAM-T99. | N | Y. Multiple sequence alignments re-threaded onto template to assess structural alignments. | N | N | Y. Metaserver uses BLAST, 3D-PSSM, mGenTHREADER, FUGUE, SAM-T99 and JPred2. | N | Y. Pair potential derived from PKB (sidechain/sidechain interactions only). | N. Only when the model was built using MODELLER. | Main difference between this group and group 450 is choice of template. |
| GeneSilico | 517 | Y | N | Y. Consensus based on PSIPred, PHD, PROF, APSSP, Jpred, SSPRO. | Y. Manual intervention at all stages, including generation of hybrid templates, alignment refinement, and partial rebuilding of backbone and sidechains. | Y | Y. Fold recognition servers and secondary structure prediction; sequences split manually. | Y. Fragments from original fold recognition models, which were positively evaluated using Verify3D. | N. Used GeneSilico server. | N | N | N | Modified fold recognition approach, selecting best supersecondary structures, optimizing and merging manually. |