Introduction
CASP experiments aim at establishing the current state of the art in
protein structure prediction, identifying what progress has been
made, and highlighting where future effort may be most productively
focused.
There have been three previous experiments, in 1994, 1996 and 1998. Full
details of these may be found at the CASP web site,
and in the special issues of the
journal PROTEINS: 23(5), 1995; Suppl 1, 1997 and Suppl 3, 1999. In
CASP3, 98 prediction groups from all around the world took part.
We now announce the fourth experiment. As before, the goal is to obtain
an in depth and objective assessment of our current abilities
and inabilities in this area. To this end, participants will predict
as much as possible about a set of soon to be known structures. These
will be true predictions, not ‘post-dictions’ made on
already known structures.
The experiment will begin in April 2000, when the first prediction
targets will be made available. The prediction season will run
through August. There will be a meeting at the Asilomar Conference
Center in California December 3 - 7th, to discuss the
results.
Scope of CASP4 and Related Experiments
As in earlier CASPs, all types of methods for predicting protein
structure will be considered, ranging from comparative modeling
through fold recognition and ab initio prediction. Most emphasis will
be on tertiary structure prediction but secondary structure and
contact prediction methods will also be included. In addition, there
will be two other experiments run in parallel with CASP4, which will
extend the scope substantially:
CAFASP2: In the era of genome sequencing, rapid protein structure modeling
methods have a critical role to play. This experiment, led by Dani
Fischer, will evaluate automatic methods of predicting protein
structure, using the CASP targets. All targets will be processed
through prediction servers that register for the experiment. Models
will be evaluated by the same numerical criteria as used for CASP4,
and a session at the CASP4 meeting will compare performance through
the servers with that obtained when full human participation is
allowed. Further details of this experiment may be found at
http://www.cs.bgu.ac.il/~dfischer/CAFASP2
CATFEE: Rational drug design can be greatly accelerated by identification and
evaluation of potential ligands in silico. This experiment, led by
Raul Cachau and Adrian Roitberg, will evaluate the state of the art
in protein ligand docking, based on bona fide predictions made on
specialized targets. There will be a meeting at Asilomar, immediately
after the CASP4 one, to assess the results. Further details of this
experiment may be found at
http://uqbar.ncifcrf.gov/~catfee/
Experiment
The broad goals of the CASP4 experiment are to address the following
questions about the current state of the art in protein structure prediction:
-
Are the models produced similar to the corresponding experimental
structure?
-
Is the mapping of the target sequence onto the proposed structure
(i.e. the alignment) correct?
-
Have similar structures that a model can be based on been identified?
-
Are the details of the models correct?
-
Has there been progress from the earlier CASPs?
-
What methods are most effective?
-
Where can future effort be most productively focused?
In addition, a set of more specific goals, based on the apparent
barriers to progress at CASP3, will be paid particular attention.
Suggested goals are:
-
Improved refinement of comparative modeling structures.
-
Accurate comparative modeling, such that functional differences
within sequence families can be deduced.
-
Improved sequence to structure alignment for all categories of model.
-
Reliable estimates of accuracy for secondary structure prediction.
-
Predictions that test hypotheses concerning the nature of the forces
and folding mechanisms.
-
Bold new methods aimed at removing current bottlenecks to progress.
The exact set of specific goals has still to be finalized, following
discussion with the consultancy groups. Participants are advised to
check for revisions.
Collection of Prediction Targets
For the experiment to succeed, it is essential that we obtain the help of
the experimental community. Therefore, starting at the beginning of
April, we will invite protein crystallographers and NMR
spectroscopists to provide details of structures they expect to have
made public before 1st October 2000.
Participation
Participation in the experiment will be open to all. Intending predictors must
register at the web site. Those interested in receiving mailings
concerning progress of the experiment may also register as
'observers' . Prediction targets will be made available through the
web site. All targets will be assigned an expiry date, and
predictions must be received and accepted before that expiration
date.
Assessment of Predictions
As in previous CASPs, independent assessors will evaluate the
predictions. There will be three assessors, representing expertise in
the comparative modeling, fold recognition and ab initio prediction
areas. Assessors will be provided with the results of numerical
evaluation of the predictions, and will judge the results primarily
on that basis. Numerical evaluation criteria have been revised from
those of earlier CASPs, and are now being finalized, in consultation
with the prediction community. The assessors will be asked to focus
particularly on the effectiveness of different methods.
Release of Results
All predictions and prediction evaluations will be made available through
this web site, shortly before the meeting.
Meeting
A meeting will be held 3-7 December, 2000 at Asilomar, California, USA
to evaluate the results of the prediction experiment. The meeting
will be limited to about 200 participants and precedence will be
given to active predictors. It is hoped that some financial
assistance will be available for the more successful predictors. The
proceedings of the meeting will be published.
Organizing Committee
John Moult,
(jmoult@tunc.org),
CARB, University of Maryland, USA
Tim Hubbard,
(th@sanger.ac.uk),
Sanger Centre, Hinxton, UK
Krzysztof Fidelis,
(fidelis@llnl.gov),
Lawrence Livermore National Laboratory, USA
Adam Zemla,
(adamz@llnl.gov),
Lawrence Livermore National Laboratory, USA
Prediction process and logistic support is provided by the Protein Structure
Prediction Center run by Krzysztof Fidelis, Adam Zemla,
and Ceslovas Venclovas (venclovas@llnl.gov).
Three Consultancy Groups of experienced predictors will provide advice
to the Organizing Committee on the details of the experiment.
Formats for Prediction Submission
General rules
The format required for submissions of CASP4 predictions.
- Predictions for CASP4 may be submitted in four separate formats:
TS # 3D atomic coordinates (Tertiary Structure) prediction
AL # Format to express unambiguous ALignments to PDB entries
SS # Secondary Structure prediction
RR # Residue-Residue separation distance prediction
- One team may make a prediction of a target by submitting
up to five models in TS/AL, SS, and RR formats (models in AL
format are considered equivalent to those in TS
format and will be translated to TS internally before evaluation).
Most of the evaluation and assessment will focus on the model labeled '1'
(model index 1, see MODEL record).
- Each submission may contain only one of the four format categories.
- Submission of each model begins with PFRMAT and ends with END record.
- Each submission may contain only one model, beginning with the MODEL record,
ending with END, and no target residue repetitions.
- Submission of a duplicate model (same target, format category, group, model
index) will replace previously accepted model, provided it is
received before the target has expired.
models in AL format are considered equivalent to those in TS format.
- Each submitted model is automatically verified by the format verification
server.
Only accepted models will be assigned an ACCESSION CODE.
A unique ACCESSION CODE is composed from the number of the target, prediction
format category, prediction group number, and model index.
Examples:
Accession code T0045SS067_1 has the following components:
T0045 target number
SS Secondary Structure prediction (PFRMAT SS)
067 prediction group 67
1 model index 1 (see MODEL record)
Accession code T0044TS005_2 has the following components:
T0044 target number
TS Tertiary Structure (3D atoms coordinates, PFRMAT TS)
005 prediction group 5
2 model index 2 (by default considered as FINAL/REFINED)
Accession code T0044TS005_2u has the following components:
T0044 target number
TS Tertiary Structure (3D atoms coordinates, PFRMAT TS)
005 prediction group 5
2u model index 2 UNREFINED set of coordinates
the CASP4 model list viewer is available
here.
All submissions contain the records described below.
Each of these records must begin with a standard keyword.
In all submissions the standard keywords must
begin in the first column of a record.
The keyword set is as follows:
PFRMAT Format specification # TS , SS , RR or AL
TARGET Target identifier from the CASP4 target table
AUTHOR XXXX-XXXX-XXXX # The registration code of the Group Leader
REMARK Comment record (may appear anywhere, optional)
METHOD Records describing the methods used
MODEL Beginning of the data section for the submitted model
PARENT Specifies structure template used to generate the TS/AL model
TER Terminates independent segments of structure in the TS/AL model
END End of the submitted model
Record PFRMAT is used for all submissions.
PFRMAT TS
TS indicates that the submission contains 3D atomic coordinates
in standard PDB format
PFRMAT SS
SS indicates that the submission contains secondary structure
prediction
PFRMAT RR
RR indicates that the submission contains residue-residue
separation distance prediction
PFRMAT AL
AL indicates that the submission contains unambiguous alignments
to PDB entries
Record TARGET is used for all submissions.
TARGET Txxxx
Txxxx indicates the id of the target predicted.
Targets from the CASP4 target list are valid.
for some targets the residue numbering can be not standard. Please
check residue numbering in "Template PDB file" provided for each
Txxxx target from CASP4 "Target list".
Record AUTHOR is used for all submissions.
AUTHOR XXXX-XXXX-XXXX
XXXX-XXXX-XXXX indicates the Group Leader's registration code.
This code is the prediction submission code obtained upon
registration at the CASP4 WEB sites (Prediction Center).
Members of prediction groups who intend to submit predictions
should use the registration code of the Group Leader for all
predictions submitted by that group.
REMARK Optional. PDB style 'REMARK' records may be used
anywhere in the submission. These records may contain any
text and will in general not influence evaluation.
Records METHOD are used for all submissions.
These records describe the methods used. Predictors are urged to provide
as full a description of the methods as possible, including references,
data libraries used, and values of non-default parameters.
These descriptions will be made available via the Prediction Center WEB
pages as well as printed along with the other materials distributed at the
meeting. Length of 100 - 500 words is suggested.
Record MODEL is used for all submissions.
Signifies the beginning of model data (3D atomic coordinates, an unambiguous
alignment to a PDB entry, residue-residue separation distance prediction,
or secondary structure prediction).
MODEL n [REFINED|UNREFINED]
n Model index n is used to indicate predictor's ranking
according to her/his belief which model is closest to the
target structure (1 <= n <= 5). Model index is included
automatically in the ACCESSION CODE.
REFINED The set of coordinates labeled REFINED will be considered
as a final model (to allow the evaluation of the results
of an automated refinement process, such as molecular
dynamics). Models submitted without any label: REFINED or
UNREFINED will be considered by default as final.
UNREFINED Coordinates labeled UNREFINED will be compared only to
the final set (REFINED) with the same model index n, to
evaluate the effectiveness of the refinement method. If
UNREFINED model is submitted, a REFINED model must be
submitted as well. The letter "u" will be added to the
model index in the ACCESSION CODE of the UNREFINED model.
Record PARENT is used for all submissions in the TS (and AL)
format.
PARENT record indicates structure templates used to generate any independent
segment of MODEL (see description of the TS format below).
The PARENT record should be placed as the first record of any such independent
segment. Only one PARENT record per structure segment is allowed.
PARENT N/A
Indicates an ab initio prediction, not directly based on any known
structure. Note that this is the only indication in the file that the
prediction is ab initio, so is a critical piece of information.
PARENT NONE [n1 n2]
Indicates that the predictor believes that there is no structure in
the present PDB that is close enough to be used as a template. This
is an entry requested by those predictors who use threading and
sequence comparison methods. With structural genomics projects being
designed to determine the structure of proteins with novel folds, the
ability to predict when a fold is unknown is becoming increasingly
important, and predictors are urged to make such submissions.
Delimiters n1 n2 indicate the range of the target sequence predicted
as having no homologue in the current PDB.
Omission of n1 n2 indicates the entire target (see Example 1 (C)).
PARENT mabc_A
Indicates that the model or the independent segment of structure is
based on a single PDB entry mabc chain A (use _A to indicate chain A).
Most threading and sequence search submissions would now be submitted
with this form of the PARENT record. A comparative modeler using a
single parent structure would also use this form. Note that, in order
to be accepted, the code must correspond to a current PDB entry.
PARENT mcdc ndef_g [ohij_k ...]
Is used only in comparative modeling and indicates that the model is
based on more than one structure template. Up to five PDB chains
may be listed here with additional detailed information included in
the METHOD records. In threading and sequence search, subdomains of
the target structure found to correspond to different known folds
should be submitted as independent segments of structure with
reference to only one PDB chain per segment.
Record TER is used to terminate an independent segment of structure
(PFRMAT TS and PFRMAT AL).
TER
3D atomic coordinates (PFRMAT TS).
Standard PDB atom records are used for the atomic coordinates. Format of the
submission requires that 80 column long records are used. These may be spaces
when needed (see target template PDB files as provided in specific target
descriptions available through the
CASP4 target table). This requirement is
necessitated by some of the software used in the evaluation of predictions.
Coordinates for each model or an independent structure segment should begin
with a single PARENT record and terminate with a TER record (see above).
It is requested that coordinate data be supplied for at least all
non-hydrogen main chain atoms, i.e. the N, CA, C and O atoms of every residue.
Specifically, if only CA atoms are predicted by the method, predictors are
encouraged to build the main chain atoms for every residue before submission
to CASP. One program that can make such a conversion is
Maxsprout server of Liisa Holm and co-workers. (If only CA atoms were submitted it would not be
possible to run most of the analysis software, which would severely limit the
evaluation of that prediction.)
When multiple independent segments of structure are used in a prediction,
they will be evaluated separately with no assumption of a common
frame of reference between the segments. For any given MODEL, no target
residue may be repeated among all such independent structure
segments. In comparative modeling and in threading, potential multi-domain
nature of targets will be addressed in the evaluation even if the prediction
is made in a single frame of reference (i.e. without separation into multiple
segments of structure). For such predictions segmentation should only be
used to allow multiple model predictions (effectively up to 5 predictions
for each such domain).
Notes:
- atoms for which a prediction has been made must contain "1.0" in
the occupancy field; those for which no prediction is made must
either contain "0.0" in that field or be skipped altogether
- error estimates, in Angstroms, must be provided in the temperature
factor field
An unambiguous alignment to a PDB entry used for threading predictions
(PFRMAT AL).
Alignment for each model or an independent structure segment should begin
with a single PARENT record and terminate with a TER record (see above).
The (four column) alignment data records provide: target residue one
letter symbol, target residue sequence number, PDB residue one letter symbol,
and PDB residue sequence number with an insertion code if necessary
(see Example 4):
aa1 n1 aa2 n2
Note:
- residues for which no prediction is made must be skipped
- if a chain ID is specified in the PDB template of the target, then
the target residue sequence number should be composed of a chain ID
and residue number, e.g. A2, B44
The PDB code with chain extension of the structure the alignment is based on
should be placed in the PARENT record.
Only one PDB code per independent structure segment is allowed.
PDB codes should refer to structures containing at least main chain atomic
coordinates (see TS format).
As in the coordinate submissions,
when multiple independent segments of structure are used in a prediction,
they will be evaluated separately with no assumption of a common
frame of reference between the segments. For any given MODEL, no target
residue may be repeated among all such independent structure
segments. Potential multi-domain
nature of targets will be addressed in the evaluation even if the prediction
is made in a single frame of reference (i.e. without separation into multiple
segments of structure). For such predictions segmentation should only be
used to allow multiple model predictions (effectively up to 5 predictions
for each such domain).
The facility to translate sequence - structure alignments (AL format) into
standard PDB atom records (TS format) is available as an additional
AL2TS service.
Secondary structure prediction (PFRMAT SS).
Data in this format is inserted between MODEL and END
records of the submission file.
The (three column) format record consists of residue code, secondary structure
assignment code, and a number specifying the associated confidence level:
aa ss p
The symbols for
the 3 state secondary structure are 'H'=helix, 'E'=strand, 'C'=Coil.
Confidence level is a probability of a residue being predicted correctly
with values in the range of 0.0 - 1.0. The entire sequence of the target should
always be given. If parts cannot be predicted a probability of 0.0 should be
used.
Residue-Residue separation prediction (PFRMAT RR).
Data in this format is inserted between MODEL and END records of the
submission file.
Format for the predicted separation distance between pairs of residues.
The distance is defined as the separation between C-beta atoms (C-alpha for
glycine residues).
Due to the fact, that the RR contact prediction evaluation issues are still
not finalized by the Consultancy Group and the dedline for the first target
is approaching, the
CASP3 format will be extended for CASP4. However it is STRONGLY recommended
that the full flexibility of the format is not used, to allow a simple and
uniform evaluation.
Thus values of d1 = 0 and d2 = 8 are recommended.
If it is planned to submit using other distance ranges (d1,d2) we request
that a corresponding prediction with only the (0,8) ranges is submitted as
model "1", and the original prediction as model "2" with the appropriate
explanation in the REMARK field regarding the relation to model "1".
The (five column) RR format:
i j d1 d2 p
Notes (see Example 3):
- entire target sequence should be split over multiple lines with a
maximum of 50 residues per line
- for intrachain residue-residue contacts residue number indices
i and j should be used for distance specification (i < j), i.e.
only one diagonal of the separation matrix should be supplied
- the distances d1 and d2 (real numbers) should indicate the range of
Cb-Cb distance predicted for the residue pair (C-alpha for glycines)
- the real number p should range from 0.0 - 1.0 to indicate
probability of the distance falling between the predicted range
- residue 'contacts' (defined here - as in CASP2 - as Cb-Cb<8A) can be
predicted with this format as:
i j 0 8 p
- any pair NOT listed is assumed to be NOT considered by predictor
- to evaluate the subset of residue-residue separation distances that
represent 'contacts', 4 separation interval bins will be used (as
in CASP2) (separation is calculated along the chain as a number of
residues between the residues in contact):
1 residue or more : 1-9999
from 1 to 4 residues : 1-4
from 5 to 8 residues : 5-8
9 residues or more : 9-9999
Example: Let's assume that two residues are in contact and there
are 6 residues in between them along the chain. This contact will
be classified as belonging to 5-8 separation interval bin and will
not be counted in 1-4 and 9-9999 bins
- in addition, in the evaluation of each prediction, 'p' will be
compared to what would be expected from random, i.e. the likelyhood
observed in the database of protein structures for a pair of
residues with residue separation (distance) d1-d2; residue
separation (sequence) j-i; protein size; types of residue i, j.
END record is used for all predictions and indicates the end of a
single model submission.
Predictions of multichain targets.
Atomic coordinates should contain chain IDs as provided in template files.
In residue-residue contact predictions residue
indices should be composed of chain ID and residue number, e.g. A2, B44
(see Example 5).
Example 1. Atomic coordinates (Tertiary Structure)
The primary CASP4 format used for comparative modeling, threading and ab initio
submission categories.
(A) An example of comparative modeling prediction. As this model is labeled
UNREFINED, submission of a
REFINED model is also required.
PFRMAT TS
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1 UNREFINED
PARENT 1abc 1def_A
ATOM 1 N GLU 1 10.982 -9.774 1.377 1.00 0.50
ATOM 2 CA GLU 1 9.623 -9.833 1.984 1.00 0.50
ATOM 3 C GLU 1 8.913 -11.104 1.521 1.00 0.50
ATOM 4 O GLU 1 9.187 -11.630 0.461 1.00 0.50
ATOM 5 CB GLU 1 8.814 -8.614 1.546 1.00 0.50
ATOM 6 CG GLU 1 7.372 -8.754 2.039 1.00 0.50
ATOM 7 CD GLU 1 7.339 -8.625 3.562 1.00 0.50
ATOM 8 OE1 GLU 1 8.370 -8.307 4.131 1.00 0.50
ATOM 9 OE2 GLU 1 6.284 -8.846 4.132 1.00 0.50
ATOM 10 N THR 2 7.998 -11.599 2.304 1.00 1.60
ATOM 11 CA THR 2 7.266 -12.832 1.907 1.00 1.60
ATOM 12 C THR 2 6.096 -12.456 1.005 1.00 1.60
ATOM 13 O THR 2 5.008 -12.217 1.466 1.00 1.60
ATOM 14 CB THR 2 6.731 -13.533 3.157 1.00 1.60
ATOM 15 OG1 THR 2 7.662 -13.379 4.220 1.00 1.60
ATOM 16 CG2 THR 2 6.526 -15.019 2.864 1.00 1.60
ATOM 17 N VAL 3 6.308 -12.396 -0.278 1.00 1.70
ATOM 18 CA VAL 3 5.190 -12.030 -1.187 1.00 1.70
ATOM 19 C VAL 3 3.954 -12.870 -0.844 1.00 1.70
ATOM 20 O VAL 3 2.834 -12.471 -1.090 1.00 1.70
ATOM 21 CB VAL 3 5.608 -12.274 -2.641 1.00 1.70
ATOM 22 CG1 VAL 3 5.542 -13.771 -2.959 1.00 1.70
ATOM 23 CG2 VAL 3 4.664 -11.514 -3.573 1.00 1.70
ATOM 24 N GLU 4 4.146 -14.029 -0.272 1.00 1.70
ATOM 25 CA GLU 4 2.976 -14.882 0.086 1.00 1.60
ATOM 26 C GLU 4 2.153 -14.190 1.175 1.00 1.50
ATOM 27 O GLU 4 0.942 -14.141 1.109 1.00 1.40
ATOM 28 CB GLU 4 3.465 -16.238 0.597 1.00 1.30
ATOM 29 CG GLU 4 2.336 -17.264 0.479 1.00 1.20
ATOM 30 CD GLU 4 2.929 -18.671 0.391 1.00 1.10
ATOM 31 OE1 GLU 4 4.056 -18.846 0.823 1.00 1.00
ATOM 32 OE2 GLU 4 2.246 -19.551 -0.108 1.00 0.90
TER
END
(B) A model consisting of 2 independent structure segments (could be a target
modeled from two PDB domains, where relative orientation is unknown;
could be 2 fragments predicted by ab initio methods - ab initio example shown).
In a single MODEL no residue should appear twice among all such segments.
PFRMAT TS
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 1 N GLU 1 10.982 -9.774 1.377 1.00 0.50
ATOM 2 CA GLU 1 9.623 -9.833 1.984 1.00 0.50
ATOM 3 C GLU 1 8.913 -11.104 1.521 1.00 0.50
ATOM 4 O GLU 1 9.187 -11.630 0.461 1.00 0.50
ATOM 5 CB GLU 1 8.814 -8.614 1.546 1.00 0.50
ATOM 6 CG GLU 1 7.372 -8.754 2.039 1.00 0.50
ATOM 7 CD GLU 1 7.339 -8.625 3.562 1.00 0.50
ATOM 8 OE1 GLU 1 8.370 -8.307 4.131 1.00 0.50
ATOM 9 OE2 GLU 1 6.284 -8.846 4.132 1.00 0.50
ATOM 10 N THR 2 7.998 -11.599 2.304 1.00 1.60
ATOM 11 CA THR 2 7.266 -12.832 1.907 1.00 1.60
ATOM 12 C THR 2 6.096 -12.456 1.005 1.00 1.60
ATOM 13 O THR 2 5.008 -12.217 1.466 1.00 1.60
ATOM 14 CB THR 2 6.731 -13.533 3.157 1.00 1.60
ATOM 15 OG1 THR 2 7.662 -13.379 4.220 1.00 1.60
ATOM 16 CG2 THR 2 6.526 -15.019 2.864 1.00 1.60
ATOM 24 N GLU 4 4.146 -14.029 -0.272 1.00 1.70
ATOM 25 CA GLU 4 2.976 -14.882 0.086 1.00 1.60
ATOM 26 C GLU 4 2.153 -14.190 1.175 1.00 1.50
ATOM 27 O GLU 4 0.942 -14.141 1.109 1.00 1.40
ATOM 28 CB GLU 4 3.465 -16.238 0.597 1.00 1.30
ATOM 29 CG GLU 4 2.336 -17.264 0.479 1.00 1.20
ATOM 30 CD GLU 4 2.929 -18.671 0.391 1.00 1.10
ATOM 31 OE1 GLU 4 4.056 -18.846 0.823 1.00 1.00
ATOM 32 OE2 GLU 4 2.246 -19.551 -0.108 1.00 0.90
TER
PARENT N/A
ATOM 17 N VAL 3 6.308 -12.396 -0.278 1.00 1.70
ATOM 18 CA VAL 3 5.190 -12.030 -1.187 1.00 1.70
ATOM 19 C VAL 3 3.954 -12.870 -0.844 1.00 1.70
ATOM 20 O VAL 3 2.834 -12.471 -1.090 1.00 1.70
ATOM 21 CB VAL 3 5.608 -12.274 -2.641 1.00 1.70
ATOM 22 CG1 VAL 3 5.542 -13.771 -2.959 1.00 1.70
ATOM 23 CG2 VAL 3 4.664 -11.514 -3.573 1.00 1.70
TER
END
(C) Threading/Fold Recognition prediction stating that target has no
homologue in the current PDB.
PFRMAT TS
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT NONE
TER
END
Example 2. Secondary structure prediction
Example of secondary structure prediction.
Note to predictors: it may be interesting to predict the secondary structure
of proteins even when a clear structural homologue is known for the target.
In cases where the target sequence is divergent from the template,
secondary structure prediction may be more accurate than that implied by the
template and visa versa.
PFRMAT SS
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
H E 0.70 # <- residue code,
L E 0.80 # <- secondary structure assignment code,
E E 0.80 # <- the number specifying the associated
G E 0.60 # confidence level
S C 0.90
I E 0.50
G E 0.40
I E 0.60
L E 0.70
L C 0.50
K C 0.50
K H 0.90
H H 0.90
E H 0.90
I H 0.80
V H 0.70
F C 0.90
D C 0.90
G H 0.40
C C 0.40
END
Example 3. Residue-Residue contact prediction
The flexibility offered by the new format allows algorithms
parameterized to predict any distance range to be used.
Below is an example of how to use the new residue-residue separation
distance format to submit a prediction of residue contacts defined as Cb-Cb
distances < 8 A.
PFRMAT RR
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC # <- entire target sequence (up to 50
HDFGRTYIWQMSD # residues per line)
1 9 0 8 0.70
1 10 0 8 0.70 # <- indices of residues: i and j (integers),
1 12 0 8 0.60 # <- the range of Cb-Cb distance predicted
1 14 0 8 0.20 # for the residue pair: d1 and d2 (real),
1 15 0 8 0.10 # <- probability of the distance between
1 17 0 8 0.30 # Cb atoms being within the specified
1 19 0 8 0.50 # range: p (real)
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
3 14 0 8 0.70
3 15 0 8 0.30
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
Example 4. An alternative alignment format for Threading/Fold Recognition
predictions
Alignments will be converted into a 3D structures.
(A) Format to express unambiguous alignments to PDB entries
'mabc_A' and 'nefg'.
PFRMAT AL
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT mabc_A
M 21 V 11
P 22 D 12
N 23 A 12A
F 24 F 12B
A 25 L 13
P 32 D 22
N 33 A 23
F 34 F 24
A 35 L 25
TER
PARENT nefg
E 75 T 73
T 76 T 74
V 77 A 75
D 78 D 76
G 79 D 77
R 80 R 78
TER
END
(B) Format to express unambiguous alignments to PDB entry 'mabc_D'.
An example of how to use the AL format to submit a prediction of
the target with a chain name of 'A'.
PFRMAT AL
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT mabc_D
M A21 V 11
P A22 D 12
N A23 A 12A
F A24 F 12B
A A25 L 13
P A32 D 22
N A33 A 23
F A34 F 24
A A35 L 25
TER
END
Example 5. Predictions of multichain targets (chains A and B)
(A) An example of 3D atomic coordinates model prediction.
PFRMAT TS
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 17 N VAL A 3 6.308 -12.396 -0.278 1.00 1.70
ATOM 18 CA VAL A 3 5.190 -12.030 -1.187 1.00 1.70
ATOM 19 C VAL A 3 3.954 -12.870 -0.844 1.00 1.70
ATOM 20 O VAL A 3 2.834 -12.471 -1.090 1.00 1.70
ATOM 21 CB VAL A 3 5.608 -12.274 -2.641 1.00 1.70
ATOM 22 CG1 VAL A 3 5.542 -13.771 -2.959 1.00 1.70
ATOM 23 CG2 VAL A 3 4.664 -11.514 -3.573 1.00 1.70
ATOM 24 N GLU A 4 4.146 -14.029 -0.272 1.00 1.70
ATOM 25 CA GLU A 4 2.976 -14.882 0.086 1.00 1.60
ATOM 26 C GLU A 4 2.153 -14.190 1.175 1.00 1.50
ATOM 27 O GLU A 4 0.942 -14.141 1.109 1.00 1.40
ATOM 28 CB GLU A 4 3.465 -16.238 0.597 1.00 1.30
ATOM 29 CG GLU A 4 2.336 -17.264 0.479 1.00 1.20
ATOM 30 CD GLU A 4 2.929 -18.671 0.391 1.00 1.10
ATOM 31 OE1 GLU A 4 4.056 -18.846 0.823 1.00 1.00
ATOM 32 OE2 GLU A 4 2.246 -19.551 -0.108 1.00 0.90
REMARK
REMARK NOTE: Predictor should NOT use TER separator between chains
REMARK if multichain independent segment of structure has to
REMARK be evaluated as a one fragment
REMARK
ATOM 1 N GLU B 1 10.982 -9.774 1.377 1.00 0.50
ATOM 2 CA GLU B 1 9.623 -9.833 1.984 1.00 0.50
ATOM 3 C GLU B 1 8.913 -11.104 1.521 1.00 0.50
ATOM 4 O GLU B 1 9.187 -11.630 0.461 1.00 0.50
ATOM 5 CB GLU B 1 8.814 -8.614 1.546 1.00 0.50
ATOM 6 CG GLU B 1 7.372 -8.754 2.039 1.00 0.50
ATOM 7 CD GLU B 1 7.339 -8.625 3.562 1.00 0.50
ATOM 8 OE1 GLU B 1 8.370 -8.307 4.131 1.00 0.50
ATOM 9 OE2 GLU B 1 6.284 -8.846 4.132 1.00 0.50
ATOM 10 N THR B 2 7.998 -11.599 2.304 1.00 1.60
ATOM 11 CA THR B 2 7.266 -12.832 1.907 1.00 1.60
ATOM 12 C THR B 2 6.096 -12.456 1.005 1.00 1.60
ATOM 13 O THR B 2 5.008 -12.217 1.466 1.00 1.60
ATOM 14 CB THR B 2 6.731 -13.533 3.157 1.00 1.60
ATOM 15 OG1 THR B 2 7.662 -13.379 4.220 1.00 1.60
ATOM 16 CG2 THR B 2 6.526 -15.019 2.864 1.00 1.60
TER
END
(B) An example of how to use the RR format to submit a prediction of
interchain (chains A and B) residue-residue contacts defined as Cb-Cb
distances < 8 A.
PFRMAT RR
TARGET Txxxx
AUTHOR xxxx-xxxx-xxxx
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC # <- entire target sequence (up to 50
HDFGRTYIWQMSD # residues per line)
A1 B9 0 8 0.70
A1 B10 0 8 0.70 # <- indices of residues: Ai and Bj,
A1 B12 0 8 0.60 # <- the range of Cb-Cb distance predicted
A1 B14 0 8 0.20 # for the residue pair: d1 and d2 (real),
A1 B15 0 8 0.10 # <- probability of the distance between
A1 B17 0 8 0.30 # Cb atoms being within the specified
A1 B19 0 8 0.50 # range: p (real)
A2 B8 0 8 0.90
A3 B7 0 8 0.70
A3 B12 0 8 0.40
A3 B14 0 8 0.70
A3 B15 0 8 0.30
A4 B6 0 8 0.90
A7 B14 0 8 0.30
A9 B14 0 8 0.50
END
