CAFASP3 Registered Servers*

Server Type Short Description Server Developer / Person in Charge Contact e-mail Address CASP5 Server Registration

ESYP HM ESyPred3D exploits a new alignment strategy using neural networks. Alignments obtained by combining, weighting and screening several multiple alignment programs. Final structure built using MODELLER Christophe Lambert Christophe.lambert@fundp.ac.be ESyPred3D

MODZ HM Modzinger Z first searches the PDB using Psi-blast. Next, a multiple structure alignment is derived, to which the target is aligned. The fragments with most conserved sequence are used to build an initial model. The rest is built using fragments from a database Shoshana Wodak mz@ucmb.ulb.ac.be Not Registered

MODW HM ModWeb is a server for calculating homology models for individual domains for the target sequence. It can also a structure to calculate models of sequences homologous to it Andrej Sali sali@rockvax.rockefeller.edu Not Registered

MOUL HM MOULDER is a homology modeling server Andrej Sali sali@rockvax.rockefeller.edu Not Registered

JIGS HM 3D-Jigsaw looks for homologous templates in a sequence databases (PFAM+PDB+nr) and splits the query sequence into domains. If good templates are found, the best covered domain is then modelled using a maximum of 2 Paul Bates paul.bates@cancer.org.uk 3D-JIGSAW

FAMS HM FAMS is a homology modeling server Hideaki Umeyama iwadatem@pharm.kitasato-u.ac.jp FAMS

FAMD HM FAMSD is a new version of FAMS Hideaki Umeyama iwadatem@pharm.kitasato-u.ac.jp FAMSD

PRCM HM PROTINFO-CM is the HM part of the PROTINFO server. The CM component does a sequence-only search to build a multiple alignment. Initial models are then built from templates and scored. Loops and side chains are built on the best models using a frozen approximation. Ram Samudrala ram@compbio.washington.edu PROTINFO-CM

TSUN HM TSUNAMI uses a BLAST-like algorithm enhanced with statistical potentials to search a structural database. A number of recognized homologous fragments is used to construct a final model Piotr Rotkiewicz piro@chem.uw.edu.pl Tsunami

ALAX HM Alax is a new sequence alignment method based on solvent accessibilities of template structures. Final structures are built using the homology modeling program FAMS Mitiko Go alax@biol1.bio.nagoya-u.ac.jp ALAX

PCOB HM/FR Pcomb uses a combination of psi-blast, profile-profile and predictions based alignments methods to create template alignments for homology. modelling Arne Elofsson arne@sbc.su.se Pcomb

PRFR FR PROTINFO-FR is the FR part of the PROTINFO server. The RAMP software uses a de novo method for generating a particular fold. Now we use CM methods to identify tenuous sequence relationships. Once a template has been chosen, it is used as a beacon to guide our simulations and a large number of structures are generated and the best scoring is selected Ram Samudrala ram@compbio.washington.edu PROTINFO-FR

RAPT FR RAPTOR uses a protein threading technique to do fold recognition via minmizing an energy function consisting of mutation, singleton, pairwise, secondary structure items. The problem is formulated as a large scale integer programming problem. Finally SVM technique is used to assess the alignment reliability Ming Li j3xu@math.uwaterloo.ca RAPTOR

MPAL FR MPALIGN combines various alignment methods. PSI-blast for easy targets. For the others, DP based sequence-to-profile alignment, using profiles from (i) PSI-search from each representative sequence, (ii) multiple profiles from sequences in the same fold, (iii) combination of (i) and profiles from structurally similar fragments. Alignment scores against many sequences are considered for selecting a template. Tatsuya Akutsu takutsu@kuicr.kyoto-u.ac.jp MPALIGN

PFIN ? PROTFINDER aligns the sequences to structures in the PDB_SELECT set. Scores result from an effective contact energy plus gap penalty terms. Near optimal alignments constructed through the Build-up algorithm (Park and Levitt, 1994). Dr Ugo Bastolla bastollau@inta.es Protfinder

CMAP ? CMap23Dpro is a contact 2d and 3d structure prediction server Gianluca Pollastri gpollast@ics.uci.edu CMap23Dpro

ARBY FR ARBY is a compute intensive method from Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Ingolf Sommer ingolf.sommer@scai.fhg.de arby-scai

PROS FR PROSPECT uses threading based methodology to carry out protein fold recognition Ying Xu x9m@ornl.gov ORNL-PROSPECT

FFAS FR FFAS compares sequence profiles with each other. Profiles are generated for protein families in a different way than in PSI-Blast but PSI-Blast is used to collect the proteins of a family. The official version from the Burnham institute is used here Leszek Rychlewski leszek@bioinfo.pl FFAS

FFA3 FR FFAS03 is based on profile-profile comparison algorithm, similar to algorithm used in FFAS and Basic family of methods. Most important differences are in calculation of profile-profile matching and in empirical evaluation of significance. FFAS03 was created at Godzik Lab at The Burnham Institute Lukasz Jaroszewki lukasz@ljcrf.edu FFAS03

FOR1 FR FORTE1 is a profile-based fold recognition program Kentaro Tomii k-tomii@aist.go.jp FORTE1

LOOP FR LOOPP (Learning, Observing and Outputting Protein Patterns) aligns sequence to sequence, sequence to structure, and structure to structure. It further enables the optimization of potentials and scoring functions for the above applications Ron Elber loopp@tc.cornell.edu Ron-Elber

ORFs FR ORFeus is based on the alignment of two profiles, which include sequence information from the family and predicted secondary structure. ORFb is used to search for the initial family Leszek Rychlewski leszek@bioinfo.pl BioInfo.PL-ORFeus

BasB FR BASIC bilaterally amplified sequence information comparison. Version B is very conservative. It uses only 3 PSI-Blast iterations Leszek Rychlewski leszek@bioinfo.pl BioInfo.PL-BasicB

BasC FR BASIC bilaterally amplified sequence information comparison. Version C is very aggressive. It uses 7 PSI-Blast iterations and RPS-Blast
Leszek Rychlewski leszek@bioinfo.pl BioInfo.PL-BasicC
ST99 FR Sam-T99 builds a multiple alignment by iterated search using HMMs to predict secondary structure and to build an HMM used for searching the PDB. Also, a library of HMMs is used to score the target sequence Kevin Karplus karplus@soe.ucsc.edu SAM-T99

ST02 FR Sam-T02 new version of the Sam-T server Kevin Karplus karplus@soe.ucsc.edu SAM-T02-server

SFAM FR SUPERFAMILY is a library of HMMs based on SCOP. Aimed at assigning SCOP domains to sequences at the superfamily level. Uses SAM software; updated with each SCOP release Julian Gough jgough@mrc-lmb.cam.ac.uk SUPERFAMILY

SFPP FR SUPFAM_PP is the next generation of SUPERFAMILY. Designed for whole genome analysis, it uses an HMM-based profile-profile comparison method Julian Gough jgough@mrc-lmb.cam.ac.uk SUPFAM_PP

3DPS FR 3D-PSSM is based on a threading approach using 1D and 3D profiles coupled with secondary structure and solvation potential. Updates its fold library every week Lawrence Kelley L.A.kelley@ic.ac.uk 3D-PSSM

GETH FR GenTHREADER combines various methods including sequence alignment with structure based scoring functions and it uses a neural network based jury system to calculate the final score for the alignment David Jones David.Jones@cs.ucl.ac.uk GenTHREADER

MGTH FR mGenTHREADER is an enhanced version of GETH. It takes as input a PSI-BLAST profile calculated for the target sequence David Jones David.Jones@cs.ucl.ac.uk mGenTHREADER

FUG2 FR FUGUE uses environment-specific substitution tables derived from the HOMSTRAD database, along with structure-dependent gap penalties, to construct profiles. FUGUE2 is an enhanced version of FUGUE, where the structural profiles are enriched by homologous sequences. Kenji Mizuguchi kenji@cryst.bioc.cam.ac.uk FUGUE2

FUG3 FR FUGUE3 is a new experimental version of FUGUE, which uses a slightly different profile library. Kenji Mizuguchi kenji@cryst.bioc.cam.ac.uk FUGUE3

INBG FR INBGU combines 5 methods which exploit sequence and structure information in different ways to produce a consensus prediction of the 5. Uses predicted vs observed secondary structure and sequence profiles. Daniel Fischer dfischer@cs.bgu.ac.il INBGU

SHGU FR ShotGun-INBGU uses the ShotGun method utilizing the INBGU components. It assembles hybrid models from INBGU. Daniel Fischer dfischer@cs.bgu.ac.il 3D-SHOTGUN-INBGU

RPFD FR RPFOLD is a hybrid method, using various sequence similarity techniques (like SSEARCH & PSI-BLAST) and secondary structure information Raghava raghava@imtech.res.in RPFOLD/ Raghava-Garjendra

BLAS FR Simple Blast to search for trivial homologs in the PDB. Runs locally at bioinfo.pl Leszek Rychlewski leszek@bioinfo.pl Not Registered

PDBb FR PDB-Blast is based on the PSI-Blast program. Before the fifth iteration the sequence profile is saved and used as query against the PDB sequences. Runs locally at bioinfo.pl Leszek Rychlewski leszek@bioinfo.pl BioInfo.PL-PDB-Blast

ORFb FR ORF-Blast uses the Blast tools for iterative search for homologs in PDB (as PDB-Blast). The initial family of homologs is built using RPS-Blast. It is expanded using 5 iterations of PSI-Blast on nr (nr70) Leszek Rychlewski leszek@bioinfo.pl BioInfo.PL-ORFblast

PRAB AI PROTINFO-AB is the ab initio part of PROTINFO. Shorter sequences without related templates, are modelled using de novo methods. Ram Samudrala ram@compbio.washington.edu PROTINFO-AB

Server	Type	Short Description	Server Developer / Person in Charge	Contact e-mail Address	CASP5 Server Registration
ESYP	HM	ESyPred3D exploits a new alignment strategy using neural networks. Alignments obtained by combining, weighting and screening several multiple alignment programs. Final structure built using MODELLER	Christophe Lambert	Christophe.lambert@fundp.ac.be	ESyPred3D
MODZ	HM	Modzinger Z first searches the PDB using Psi-blast. Next, a multiple structure alignment is derived, to which the target is aligned. The fragments with most conserved sequence are used to build an initial model. The rest is built using fragments from a database	Shoshana Wodak	mz@ucmb.ulb.ac.be	Not Registered
MODW	HM	ModWeb is a server for calculating homology models for individual domains for the target sequence. It can also a structure to calculate models of sequences homologous to it	Andrej Sali	sali@rockvax.rockefeller.edu	Not Registered
MOUL	HM	MOULDER is a homology modeling server	Andrej Sali	sali@rockvax.rockefeller.edu	Not Registered
JIGS	HM	3D-Jigsaw looks for homologous templates in a sequence databases (PFAM+PDB+nr) and splits the query sequence into domains. If good templates are found, the best covered domain is then modelled using a maximum of 2	Paul Bates	paul.bates@cancer.org.uk	3D-JIGSAW
FAMS	HM	FAMS is a homology modeling server	Hideaki Umeyama	iwadatem@pharm.kitasato-u.ac.jp	FAMS
FAMD	HM	FAMSD is a new version of FAMS	Hideaki Umeyama	iwadatem@pharm.kitasato-u.ac.jp	FAMSD
PRCM	HM	PROTINFO-CM is the HM part of the PROTINFO server. The CM component does a sequence-only search to build a multiple alignment. Initial models are then built from templates and scored. Loops and side chains are built on the best models using a frozen approximation.	Ram Samudrala	ram@compbio.washington.edu	PROTINFO-CM
TSUN	HM	TSUNAMI uses a BLAST-like algorithm enhanced with statistical potentials to search a structural database. A number of recognized homologous fragments is used to construct a final model	Piotr Rotkiewicz	piro@chem.uw.edu.pl	Tsunami
ALAX	HM	Alax is a new sequence alignment method based on solvent accessibilities of template structures. Final structures are built using the homology modeling program FAMS	Mitiko Go	alax@biol1.bio.nagoya-u.ac.jp	ALAX
PCOB	HM/FR	Pcomb uses a combination of psi-blast, profile-profile and predictions based alignments methods to create template alignments for homology. modelling	Arne Elofsson	arne@sbc.su.se	Pcomb
PRFR	FR	PROTINFO-FR is the FR part of the PROTINFO server. The RAMP software uses a de novo method for generating a particular fold. Now we use CM methods to identify tenuous sequence relationships. Once a template has been chosen, it is used as a beacon to guide our simulations and a large number of structures are generated and the best scoring is selected	Ram Samudrala	ram@compbio.washington.edu	PROTINFO-FR
RAPT	FR	RAPTOR uses a protein threading technique to do fold recognition via minmizing an energy function consisting of mutation, singleton, pairwise, secondary structure items. The problem is formulated as a large scale integer programming problem. Finally SVM technique is used to assess the alignment reliability	Ming Li	j3xu@math.uwaterloo.ca	RAPTOR
MPAL	FR	MPALIGN combines various alignment methods. PSI-blast for easy targets. For the others, DP based sequence-to-profile alignment, using profiles from (i) PSI-search from each representative sequence, (ii) multiple profiles from sequences in the same fold, (iii) combination of (i) and profiles from structurally similar fragments. Alignment scores against many sequences are considered for selecting a template.	Tatsuya Akutsu	takutsu@kuicr.kyoto-u.ac.jp	MPALIGN
PFIN	?	PROTFINDER aligns the sequences to structures in the PDB_SELECT set. Scores result from an effective contact energy plus gap penalty terms. Near optimal alignments constructed through the Build-up algorithm (Park and Levitt, 1994).	Dr Ugo Bastolla	bastollau@inta.es	Protfinder
CMAP	?	CMap23Dpro is a contact 2d and 3d structure prediction server	Gianluca Pollastri	gpollast@ics.uci.edu	CMap23Dpro
ARBY	FR	ARBY is a compute intensive method from Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)	Ingolf Sommer	ingolf.sommer@scai.fhg.de	arby-scai
PROS	FR	PROSPECT uses threading based methodology to carry out protein fold recognition	Ying Xu	x9m@ornl.gov	ORNL-PROSPECT
FFAS	FR	FFAS compares sequence profiles with each other. Profiles are generated for protein families in a different way than in PSI-Blast but PSI-Blast is used to collect the proteins of a family. The official version from the Burnham institute is used here	Leszek Rychlewski	leszek@bioinfo.pl	FFAS
FFA3	FR	FFAS03 is based on profile-profile comparison algorithm, similar to algorithm used in FFAS and Basic family of methods. Most important differences are in calculation of profile-profile matching and in empirical evaluation of significance. FFAS03 was created at Godzik Lab at The Burnham Institute	Lukasz Jaroszewki	lukasz@ljcrf.edu	FFAS03
FOR1	FR	FORTE1 is a profile-based fold recognition program	Kentaro Tomii	k-tomii@aist.go.jp	FORTE1
LOOP	FR	LOOPP (Learning, Observing and Outputting Protein Patterns) aligns sequence to sequence, sequence to structure, and structure to structure. It further enables the optimization of potentials and scoring functions for the above applications	Ron Elber	loopp@tc.cornell.edu	Ron-Elber
ORFs	FR	ORFeus is based on the alignment of two profiles, which include sequence information from the family and predicted secondary structure. ORFb is used to search for the initial family	Leszek Rychlewski	leszek@bioinfo.pl	BioInfo.PL-ORFeus
BasB	FR	BASIC bilaterally amplified sequence information comparison. Version B is very conservative. It uses only 3 PSI-Blast iterations	Leszek Rychlewski	leszek@bioinfo.pl	BioInfo.PL-BasicB
BasC	FR	BASIC bilaterally amplified sequence information comparison. Version C is very aggressive. It uses 7 PSI-Blast iterations and RPS-Blast	Leszek Rychlewski	leszek@bioinfo.pl	BioInfo.PL-BasicC
ST99	FR	Sam-T99 builds a multiple alignment by iterated search using HMMs to predict secondary structure and to build an HMM used for searching the PDB. Also, a library of HMMs is used to score the target sequence	Kevin Karplus	karplus@soe.ucsc.edu	SAM-T99
ST02	FR	Sam-T02 new version of the Sam-T server	Kevin Karplus	karplus@soe.ucsc.edu	SAM-T02-server
SFAM	FR	SUPERFAMILY is a library of HMMs based on SCOP. Aimed at assigning SCOP domains to sequences at the superfamily level. Uses SAM software; updated with each SCOP release	Julian Gough	jgough@mrc-lmb.cam.ac.uk	SUPERFAMILY
SFPP	FR	SUPFAM_PP is the next generation of SUPERFAMILY. Designed for whole genome analysis, it uses an HMM-based profile-profile comparison method	Julian Gough	jgough@mrc-lmb.cam.ac.uk	SUPFAM_PP
3DPS	FR	3D-PSSM is based on a threading approach using 1D and 3D profiles coupled with secondary structure and solvation potential. Updates its fold library every week	Lawrence Kelley	L.A.kelley@ic.ac.uk	3D-PSSM
GETH	FR	GenTHREADER combines various methods including sequence alignment with structure based scoring functions and it uses a neural network based jury system to calculate the final score for the alignment	David Jones	David.Jones@cs.ucl.ac.uk	GenTHREADER
MGTH	FR	mGenTHREADER is an enhanced version of GETH. It takes as input a PSI-BLAST profile calculated for the target sequence	David Jones	David.Jones@cs.ucl.ac.uk	mGenTHREADER
FUG2	FR	FUGUE uses environment-specific substitution tables derived from the HOMSTRAD database, along with structure-dependent gap penalties, to construct profiles. FUGUE2 is an enhanced version of FUGUE, where the structural profiles are enriched by homologous sequences.	Kenji Mizuguchi	kenji@cryst.bioc.cam.ac.uk	FUGUE2
FUG3	FR	FUGUE3 is a new experimental version of FUGUE, which uses a slightly different profile library.	Kenji Mizuguchi	kenji@cryst.bioc.cam.ac.uk	FUGUE3
INBG	FR	INBGU combines 5 methods which exploit sequence and structure information in different ways to produce a consensus prediction of the 5. Uses predicted vs observed secondary structure and sequence profiles.	Daniel Fischer	dfischer@cs.bgu.ac.il	INBGU
SHGU	FR	ShotGun-INBGU uses the ShotGun method utilizing the INBGU components. It assembles hybrid models from INBGU.	Daniel Fischer	dfischer@cs.bgu.ac.il	3D-SHOTGUN-INBGU
RPFD	FR	RPFOLD is a hybrid method, using various sequence similarity techniques (like SSEARCH & PSI-BLAST) and secondary structure information	Raghava	raghava@imtech.res.in	RPFOLD/ Raghava-Garjendra
BLAS	FR	Simple Blast to search for trivial homologs in the PDB. Runs locally at bioinfo.pl	Leszek Rychlewski	leszek@bioinfo.pl	Not Registered
PDBb	FR	PDB-Blast is based on the PSI-Blast program. Before the fifth iteration the sequence profile is saved and used as query against the PDB sequences. Runs locally at bioinfo.pl	Leszek Rychlewski	leszek@bioinfo.pl	BioInfo.PL-PDB-Blast
ORFb	FR	ORF-Blast uses the Blast tools for iterative search for homologs in PDB (as PDB-Blast). The initial family of homologs is built using RPS-Blast. It is expanded using 5 iterations of PSI-Blast on nr (nr70)	Leszek Rychlewski	leszek@bioinfo.pl	BioInfo.PL-ORFblast
PRAB	AI	PROTINFO-AB is the ab initio part of PROTINFO. Shorter sequences without related templates, are modelled using de novo methods.	Ram Samudrala	ram@compbio.washington.edu	PROTINFO-AB

In addition, and in a different category, are meta-predictors which generate predictions utilizing models produced by other services.

Meta-Predictor Type Short Description Server Developer / Person in Charge Contact e-mail Address CASP5 Server Registration

CONS ? CONSENSUS predicts only the high confidence structural alignment of a target using a hybrid of other methods available in the literature Carlos Camacho ccamacho@bu.edu Camacho-Carlos

RBTA HM/AI ROBETTA provides both ab initio and comparative models of protein domains. It uses the ROSETTA fragment insertion method. Comparative models built from structures detected by PDB-BLAST or Pcons2 and aligned by the K*SYNC alignment method. David Baker dabaker@u.washington.edu BAKER-ROBETTA

HMMS AI HMMSTR, I_SITES and ROSETTA used to produce ab initio predictions using the ROSETTA Fragment Insertion Monte carlo method. The fragment moveset is made by I_SITES. Secondary structure and local structure are predicted by HMMSTR Chris Bystroff bystrc@rpi.edu I-sites/Bystroff

CNBP FR CNBPred combines results from different threading servers, among them and with other information Alfonso Valencia osvaldog@cnb.uam.es CNBpred

LBLL FR LIBELLULA obtains predictions from samt99 and 3dpssm, then a NN REevaluates with additional evolutionary information Alfonso Valencia osvaldog@cnb.uam.es LIBELLULA

PCO2 FR Pcons2 (updated Pcons) is a consensus server that utilizes the predictions from PDB-Blast, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99 and FUGUE. It selects one of the models returned by these services Arne Elofsson arne@sbc.su.se Pcons2

PCO3 FR Pcons3 (new Pcons) is a consensus server that utilizes the predictions from PDB-Blast, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99, FUGUE2, SHotGun-INBGU and ORFeus. It selects one of the models returned by these services Arne Elofsson arne@sbc.su.se Pcons3

PMOD HM/FR Pmodeller is based on Pcons2. It provides models optimized in the last step using the Modeller program Arne Elofsson arne@sbc.su.se Pmodel

PMO3 HM/FR Pmodeller3 is based on Pcons3. It provides models optimized in the last step using the Modeller program Arne Elofsson arne@sbc.su.se Pmodel3

3DS3 FR ShotGun on 3 is a meta-predictor using the ShotGun method applied to the results of FFAS, 3D-PSSM and INBGU. It assembles hybrid models from models of the 3 servers. Daniel Fischer dfischer@cs.bgu.ac.il 3D-SHOTGUN-3DS3

3DSN FR 3DSN returns the same result as 3DS3, but without the assembly Daniel Fischer dfischer@cs.bgu.ac.il 3D-SHOTGUN-3DSN

3DS5 FR ShotGun on 5 is a meta-predictor, like 3DS3, but using the results of FFAS, 3D-PSSM, SHGU, FUGUE and GenTHREADER. Daniel Fischer dfischer@cs.bgu.ac.il 3D-SHOTGUN-3DS5

Meta-Predictor	Type	Short Description	Server Developer / Person in Charge	Contact e-mail Address	CASP5 Server Registration
CONS	?	CONSENSUS predicts only the high confidence structural alignment of a target using a hybrid of other methods available in the literature	Carlos Camacho	ccamacho@bu.edu	Camacho-Carlos
RBTA	HM/AI	ROBETTA provides both ab initio and comparative models of protein domains. It uses the ROSETTA fragment insertion method. Comparative models built from structures detected by PDB-BLAST or Pcons2 and aligned by the K*SYNC alignment method.	David Baker	dabaker@u.washington.edu	BAKER-ROBETTA
HMMS	AI	HMMSTR, I_SITES and ROSETTA used to produce ab initio predictions using the ROSETTA Fragment Insertion Monte carlo method. The fragment moveset is made by I_SITES. Secondary structure and local structure are predicted by HMMSTR	Chris Bystroff	bystrc@rpi.edu	I-sites/Bystroff
CNBP	FR	CNBPred combines results from different threading servers, among them and with other information	Alfonso Valencia	osvaldog@cnb.uam.es	CNBpred
LBLL	FR	LIBELLULA obtains predictions from samt99 and 3dpssm, then a NN REevaluates with additional evolutionary information	Alfonso Valencia	osvaldog@cnb.uam.es	LIBELLULA
PCO2	FR	Pcons2 (updated Pcons) is a consensus server that utilizes the predictions from PDB-Blast, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99 and FUGUE. It selects one of the models returned by these services	Arne Elofsson	arne@sbc.su.se	Pcons2
PCO3	FR	Pcons3 (new Pcons) is a consensus server that utilizes the predictions from PDB-Blast, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99, FUGUE2, SHotGun-INBGU and ORFeus. It selects one of the models returned by these services	Arne Elofsson	arne@sbc.su.se	Pcons3
PMOD	HM/FR	Pmodeller is based on Pcons2. It provides models optimized in the last step using the Modeller program	Arne Elofsson	arne@sbc.su.se	Pmodel
PMO3	HM/FR	Pmodeller3 is based on Pcons3. It provides models optimized in the last step using the Modeller program	Arne Elofsson	arne@sbc.su.se	Pmodel3
3DS3	FR	ShotGun on 3 is a meta-predictor using the ShotGun method applied to the results of FFAS, 3D-PSSM and INBGU. It assembles hybrid models from models of the 3 servers.	Daniel Fischer	dfischer@cs.bgu.ac.il	3D-SHOTGUN-3DS3
3DSN	FR	3DSN returns the same result as 3DS3, but without the assembly	Daniel Fischer	dfischer@cs.bgu.ac.il	3D-SHOTGUN-3DSN
3DS5	FR	ShotGun on 5 is a meta-predictor, like 3DS3, but using the results of FFAS, 3D-PSSM, SHGU, FUGUE and GenTHREADER.	Daniel Fischer	dfischer@cs.bgu.ac.il	3D-SHOTGUN-3DS5

*Servers for Secondary Structure and Contacts Prediction are not yet listed.