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SERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins forRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1 HIGH ACCURACY ASSESSMENT IN CASP14 High Accuracy Assessment in CASP14 Andrei N. Lupas Joana Pereira. Marcus D. Hartmann. Max Planck Institute for Developmental Biology POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction GROUPS ANALYSIS: ZSCORES 1. Calculate z-scores from the raw scores for all "first" models (corresponding values from the main result table); 2. Remove outliers - models with zscores below the tolerance threshold (set to -2.0); 3. Recalculate z-scores on the reduced dataset; 4. Assign z-scores below the penalty threshold (either -2.0 or 0.0) to the value of thisthreshold.
POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novel HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins forRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1 HIGH ACCURACY ASSESSMENT IN CASP14 High Accuracy Assessment in CASP14 Andrei N. Lupas Joana Pereira. Marcus D. Hartmann. Max Planck Institute for Developmental Biology POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction GROUPS ANALYSIS: ZSCORES 1. Calculate z-scores from the raw scores for all "first" models (corresponding values from the main result table); 2. Remove outliers - models with zscores below the tolerance threshold (set to -2.0); 3. Recalculate z-scores on the reduced dataset; 4. Assign z-scores below the penalty threshold (either -2.0 or 0.0) to the value of thisthreshold.
POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novel HOME - CASP_COMMONS - PREDICTION CENTER CASP_Commons description. CASP_Commons is a collaborative of members of the CASP community aimed at providing the best possible models to the interested investigators in as useful and convenient a manner as possible. Note that this endeavor is not part of regular CASPexperiments.
HOME - PREDICTION CENTER PRESS RELEASE . Embargo: 15.30 hrs GMT Monday 30 November 2020 . Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research PREDICTIONCENTER.ORG 000 ; 003 SHORTLE : 005 Seder2020 : 009 tFold_human : 013 FEIG-S : 014 xianmingpan : 015 AP_1 : 018 UNRES-template : 024 DeepPotential : 026 NOVA : 029 Venclovas : 031 Zhang-CEthrGDT SUMMARY PLOT
003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-S 014 xianmingpan GROUPS ANALYSIS: ZSCORES 1. Calculate z-scores from the raw scores for all "first" models (corresponding values from the main result table); 2. Remove outliers - models with zscores below the tolerance threshold (set to -2.0); 3. Recalculate z-scores on the reduced dataset; 4. Assign z-scores below the penalty threshold (either -2.0 or 0.0) to the value of thisthreshold.
RESULTS LIST
Protein Structure Prediction Center Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS) Please address any questions or queries to: © 2007CASPCOMMONS MODELS
The S-score is a measure of proximity of corresponding residues in the LGA sequence-dependent superposition; in essence, it is the distance d between CA atoms of the corresponding residues transformed to range using the S-function=1/ (1+ (d/5)^2). The local consensus score for a residue in a model is the average of local LDDT scores or SINFO - CASP14
kyungmin cho. Hyoje Cho. Kyeongtak Han. Wonjun Lee. TS (regular targets): 402 models for 81 targets. TS (refinement targets): 247 models for 50 targets. RR REFINEMENT LOCAL ACCURACY Starting and refined models are superimposed with experimental structure using sequence-dependent LGA protocol (4A distance cutoff). Difference between the correspondingRESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novel HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novelPROCEEDINGS
Proceedings: CASP13 proceedings: Proteins: Structure, Function, and Bioinformatics. Volume 87, Issue 12, Pages 1007-1388 (2019) Table of Contents (FREE ACCESS)REGISTRATION
Registration Form. Registration with the Prediction Center is a one-time procedure, which will store the basic information about the user in our database. The information provided will not be shared with anyone outside the CASP system. It will be available for future retrieval/editing if participating in CASP experiments or using localservices.
HOME - CASP_COMMONS - PREDICTION CENTER CASP_Commons description. CASP_Commons is a collaborative of members of the CASP community aimed at providing the best possible models to the interested investigators in as useful and convenient a manner as possible. Note that this endeavor is not part of regular CASPexperiments.
PREDICTIONCENTER.ORG 000 ; 003 SHORTLE : 005 Seder2020 : 009 tFold_human : 013 FEIG-S : 014 xianmingpan : 015 AP_1 : 018 UNRES-template : 024 DeepPotential : 026 NOVA : 029 Venclovas : 031 Zhang-CEthrRESULTS LIST
Protein Structure Prediction Center Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS) Please address any questions or queries to: © 2007CASPCOMMONS MODELS
The S-score is a measure of proximity of corresponding residues in the LGA sequence-dependent superposition; in essence, it is the distance d between CA atoms of the corresponding residues transformed to range using the S-function=1/ (1+ (d/5)^2). The local consensus score for a residue in a model is the average of local LDDT scores or SRESULTS - CASP13
Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 000 3Dbio 359 3DCNN 365 3D-JIGSAW_SL1 043 A7D 007 ACOMPMOD 433 AIR 426 AP_1 321 ASDP_baseline_NoEC 313 ASDP.BEC 459 ASP_baseline_PEC 112 AWSEM REFINEMENT LOCAL ACCURACY Starting and refined models are superimposed with experimental structure using sequence-dependent LGA protocol (4A distance cutoff). Difference between the correspondingTARGETS - CASP14
Target List csv: Targets expire on the specified date at noon (12:00) local time in California (GMT - 7 hours). Green color - active target; Yellow color - target expires within 48 hours; Orange color - target expires within 24 hours; Red color - target has expired for server TS/RR predictions, but isTARGET - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novel HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novelPROCEEDINGS
Proceedings: CASP13 proceedings: Proteins: Structure, Function, and Bioinformatics. Volume 87, Issue 12, Pages 1007-1388 (2019) Table of Contents (FREE ACCESS)REGISTRATION
Registration Form. Registration with the Prediction Center is a one-time procedure, which will store the basic information about the user in our database. The information provided will not be shared with anyone outside the CASP system. It will be available for future retrieval/editing if participating in CASP experiments or using localservices.
HOME - CASP_COMMONS - PREDICTION CENTER CASP_Commons description. CASP_Commons is a collaborative of members of the CASP community aimed at providing the best possible models to the interested investigators in as useful and convenient a manner as possible. Note that this endeavor is not part of regular CASPexperiments.
PREDICTIONCENTER.ORG 000 ; 003 SHORTLE : 005 Seder2020 : 009 tFold_human : 013 FEIG-S : 014 xianmingpan : 015 AP_1 : 018 UNRES-template : 024 DeepPotential : 026 NOVA : 029 Venclovas : 031 Zhang-CEthrRESULTS LIST
Protein Structure Prediction Center Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS) Please address any questions or queries to: © 2007CASPCOMMONS MODELS
The S-score is a measure of proximity of corresponding residues in the LGA sequence-dependent superposition; in essence, it is the distance d between CA atoms of the corresponding residues transformed to range using the S-function=1/ (1+ (d/5)^2). The local consensus score for a residue in a model is the average of local LDDT scores or SRESULTS - CASP13
Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 000 3Dbio 359 3DCNN 365 3D-JIGSAW_SL1 043 A7D 007 ACOMPMOD 433 AIR 426 AP_1 321 ASDP_baseline_NoEC 313 ASDP.BEC 459 ASP_baseline_PEC 112 AWSEM REFINEMENT LOCAL ACCURACY Starting and refined models are superimposed with experimental structure using sequence-dependent LGA protocol (4A distance cutoff). Difference between the correspondingTARGETS - CASP14
Target List csv: Targets expire on the specified date at noon (12:00) local time in California (GMT - 7 hours). Green color - active target; Yellow color - target expires within 48 hours; Orange color - target expires within 24 hours; Red color - target has expired for server TS/RR predictions, but isTARGET - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novel HOME - PREDICTION CENTERFORCASPREGISTRATIONCASP11CASP14FULLY AUTOMATEDSERVERSCASP13
X-linking -assisted model 220_1. GDT_TS=52. Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. HOME - CASP14 - HOME - PREDICTION CENTER The CASP14 conference was virtual. It was held from November 30 through December 4, 2020 using Zoom, Discord, and AirMeet platforms. Every day, main sessions ran from 10am - 2pm EST (see the Program link above), with poster sessions and sattelite sessions arranged outsidethis time frame.
HOME - CASP13 - HOME - PREDICTION CENTER CASP (Critical Assessment of Structure Prediction) is a community wide experiment to determine and advance the state of the art in modeling protein structure from amino acid sequence. Every two years, participants are invited to submit models for a set of proteins for HOME - CASP_COMMONS - PREDICTION CENTERSEE MORE ON PREDICTIONCENTER.ORGRESULTS - CASP14
Results Home. Table Browser. Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 061 191227 169 3D-JIGSAW-SwarmLoop 063 ACOMPMOD 192 AILON 100 AIR 427 AlphaFold2 015 AP_1 259 AWSEM-CHEN 389 AWSEM_PCA 097 AWSEM-Suite 448 POSITION SPECIFIC ALIGNMENT 000 003 SHORTLE 005 Seder2020 009 tFold_human 013 FEIG-SRESULTS TABLE HELP
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Ã… in both cases and RMSD-cutoffs = 2Ã… and 4Ã…. For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.ALPHAFOLD 2
AlphaFold 2 John Jumper1*☨, Richard Evans1*, Alexander Pritzel1*, Tim Green1*, Michael Figurnov1*, Kathryn Tunyasuvunakool1*, Olaf Ronneberger1*, Russ Bates1RESULTS - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction POSITION SPECIFIC ALIGNMENT 043 a7d 004 yasara 007 acompmod 023 multicom-novelPROCEEDINGS
Proceedings: CASP13 proceedings: Proteins: Structure, Function, and Bioinformatics. Volume 87, Issue 12, Pages 1007-1388 (2019) Table of Contents (FREE ACCESS)REGISTRATION
Registration Form. Registration with the Prediction Center is a one-time procedure, which will store the basic information about the user in our database. The information provided will not be shared with anyone outside the CASP system. It will be available for future retrieval/editing if participating in CASP experiments or using localservices.
HOME - CASP_COMMONS - PREDICTION CENTER CASP_Commons description. CASP_Commons is a collaborative of members of the CASP community aimed at providing the best possible models to the interested investigators in as useful and convenient a manner as possible. Note that this endeavor is not part of regular CASPexperiments.
PREDICTIONCENTER.ORG 000 ; 003 SHORTLE : 005 Seder2020 : 009 tFold_human : 013 FEIG-S : 014 xianmingpan : 015 AP_1 : 018 UNRES-template : 024 DeepPotential : 026 NOVA : 029 Venclovas : 031 Zhang-CEthrRESULTS LIST
Protein Structure Prediction Center Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS) Please address any questions or queries to: © 2007CASPCOMMONS MODELS
The S-score is a measure of proximity of corresponding residues in the LGA sequence-dependent superposition; in essence, it is the distance d between CA atoms of the corresponding residues transformed to range using the S-function=1/ (1+ (d/5)^2). The local consensus score for a residue in a model is the average of local LDDT scores or SRESULTS - CASP13
Estimate of Model Accuracy Results. RR Assessment Results. Results for Group: - All Groups - 000 3Dbio 359 3DCNN 365 3D-JIGSAW_SL1 043 A7D 007 ACOMPMOD 433 AIR 426 AP_1 321 ASDP_baseline_NoEC 313 ASDP.BEC 459 ASP_baseline_PEC 112 AWSEM REFINEMENT LOCAL ACCURACY Starting and refined models are superimposed with experimental structure using sequence-dependent LGA protocol (4A distance cutoff). Difference between the correspondingTARGETS - CASP14
Target List csv: Targets expire on the specified date at noon (12:00) local time in California (GMT - 7 hours). Green color - active target; Yellow color - target expires within 48 hours; Orange color - target expires within 24 hours; Red color - target has expired for server TS/RR predictions, but isTARGET - CASP13
13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Protein Structure Prediction Center Success Stories From Recent CASPs_template-based
modeling_
_ab initio
modeling_
_contact
prediction_
_help structural
biologists_
_refinement_
_data-assisted
modeling_
||
_TEMPLATE-BASED MODELING_ Models based on templates identified by sequence similarity remain the most accurate. Over the course of the CASP experiments there have been enormous improvements in this area. However, the overall accuracy improvements that we have seen in the first 10 years of CASP remained unmatched until CASP12 (2016), when a new burst of progress happened.
In two
years from 2014 to 2016, the backbone accuracy of the submitted models improved more than in the preceeding 10 years. The next CASP continuedthe trend
, and the
2014-2018 model accuracy improvement doubled that of 2004-2014 (see the plot). Several factors contributed to this, including more accurate alignment of the target sequence to that of available templates, combining multiple templates, improved accuracy of regions not covered by templates, successful refinement of models, and better selection of models from decoy sets due to improved methods for estimation of model accuracy. target T0868-D1 (orange) model 330_2 (blue): GDT_TS=87 best template: 2cw6 (seq.id= 4.2%) _AB INITIO MODELING_ Modeling proteins with no or marginal similarity to existing structures (_ab initio, new fold, non-template_ or _free_ modeling) is the most challenging task in tertiary structure prediction. Probably the first ab initio model of reasonable accuracy was built in CASP4. Since then CASP witnessed sustained progress in ab initio prediction, but mainly for small proteins (120 residues or less, panels 1 and 2; models are in blue, targets in orange). In CASP11 for the first time a larger new fold protein (256 residues, sequence identity to known structures <5%) was built with unpresedented before accuracy for targets of this size (panel 3). CASP11 and CASP12 experiments (2014, 2016) also showed a new trend in building better non-template models by successful utilizing predicted contacts (panel 4) . CASP13 witnessed yet another substantial improvement in accuracy of template-free models mainly due to employing advanced deep learning artificial intelligence techniques coupled with prediction of inter-residue distances at a range of thresholds,
. The
best models submitted on the free modeling targets showed more than 20% increase in accuracy of the backbone, with the average GDT_TS scores going up from 52.9 in CASP12 to 65.7 in CASP13.CASP7:Â T0283-D1
model 321_1: GDT_TS=75CASP9: T0581-D1
model 170_1: GDT_TS=71CASP11: T0806-D1
model 064_1: GDT_TS=61CASP12: T0866-D1
model 325_5: GDT_TS=81 _CONTACT PREDICTION_ The most notable progress in recent CASPs (2014, 2016) resulted from sustained improvement in methods for predicting three-dimensional contacts between pairs of residues in structures. Average precision of the best CASP12 contact predictor almost doubled compared to that of the best CASP11 predictor (from 27% to 47% - see the plot). Advances in the field as a whole are not any less impressive: 26 methods in CASP12 showed better results than the best method in CASP11. Theoretical advance in contact prediction lead to improved accuracy of 3D models, especially for the hardest template-free modeling cases (see models for CASP12 target T0915 below). CASP13 (2018) registered yet another leap in accuracy of contact prediction, with the average precision of the best contact prediction group increasing by 23% (compared to CASP12) and reaching 70%. modeling without constraints modeling using predicted contacts as contsraints_predictors help
structural biologists_ CASP models help structural biologists to solve protein structure by molecular replacement. In particular, CASP models were used to solve the structure of the Sla2 protein (see an excerpt from the paper describing the structure below): "A total of 150 in silico designed models that were based on the amino acid sequence of Hip1R were provided by CASP11. One model designed by the Baker-Rosetta team gave a marginal solution, placing two molecules in the asymmetric unit of the P21 crystal form. The CASP model was derived from the CALM crystal structure (PDBID 3ZYM), but it had an RMSD of 2.0â„« for 219 residues when superimposed on the originalmodel."
T0839-D1
model:Â TS184_1Â (GDT_TS:Â 62.8)_REFINEMENT_
Refinement category assesses ability of methods to refine available models towards a more accurate representation of the experimental structure. CASP10-13 assessments showed two trends in methods development. First, some molecular dynamics methods can consistently even though very modestly improve over the starting models. A group of more aggressive refinement methods showed to be able to provide very impressive examples of substantial improvement, though at the price of consistency (occasionally models move away from the experimental structure rather than towards it). Below is are some examples of notable refinement in CASP12. The target structure is shown in orange, the starting model in green and the refined model in blue. target TR884; model 118_1starting GDT_TS=66
refined GDT_TS=76
target TR894; model 118_5starting GDT_TS=75
refined GDT_TS=96
target TR896; model 220_1starting GDT_TS=61
refined GDT_TS=77
_DATA-ASSISTED MODELING_ Data-assisted or hybrid modeling, in which low-resolution experimental data are combined with computational methods, is becoming increasing important for a range of experimental data, including NMR, chemical cross-linking and surface labeling, X-ray and neutron scattering, electron microscopy and FRET. CASP11-CASP13 experiments included a special sub-category of modeling proteins using such data. Description of the CASP12 data-assisted experiment and the data is provided in Examples of a non-assisted model and a cross-linking assisted model from the same predictor (CASP12 group 220) are shown below demonstrating increased accuracy of the assisted prediction.target T0894
original model 220_1GDT_TS=24
target Tx894
X-linking -assisted model 220_1GDT_TS=52
Welcome to the Protein Structure Prediction Center! Our goal is to help advance the methods of identifying protein structure from sequence. The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction. The Critical Assessment of protein Structure Prediction (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 thirteen previous CASP experiments. The fourteenth experiment is planned to start in April 2020. Description of these experiments and the full data (targets, predictions, interactive tables with numerical evaluation results, dynamic graphs and prediction visualization tools) can be accessed following the links:CASP1Â (1994)
| CASP2Â (1996)
| CASP3Â (1998)
| CASP4Â (2000)
| CASP5Â (2002)
| CASP6Â (2004)
| CASP7Â (2006)
| CASP8Â (2008) |
CASP9Â (2010) |
CASP10Â (2012) |
CASP11Â (2014) |
CASP12Â (2016) |
CASP13Â (2018) |
CASP14Â (2020) Raw
data for the experiments held so far are archived and stored in ourdata archive .
------------------------- Details of the experiments have been published in a scientific journal _Proteins: Structure, Function and Bioinformatics_. CASP PROCEEDINGS include papers describing the structure and conduct of the experiments, the numerical evaluation measures, reports from the assessment teams highlighting state of the art in different prediction categories, methods from some of the most successful prediction teams, and progress in various aspects of themodeling.
------------------------- Prediction methods are assessed on the basis of the analysis of a large number of blind predictions of protein structure. Summary of numerical evaluation of the tertiary structure prediction methods tested in the latest CASP experiment can be found on this web page. The main
numerical measures used in evaluations, data handling procedures, and guidelines for navigating the data presented on this website aredescribed in
.
Some of the best performing methods are implemented as fully automatedservers and
therefore can be used by public for protein structure modeling. ------------------------- To proceed to the pages related to the latest CASP experiments clickon the logo below:
------------------------- Related experiments and forums:Prediction
of docking interactions Continuous Automated Model EvaluatiOnDiscussion Forum
Message Board
QA FOR SECOND STAGE OF CASP-COVID We have posted predictions from the second stage of CASP-covidexperiment at
https://predictioncenter.org/download_area/CASPCOMMONS/2020_COVID-19/TS_predictions/stage2 We will be collecting model a ... END OF CASP-COVID STAGE 2; START OF CASP14 Dear CASPers, 1. We will stop accepting stage2 CASP-covid structural predictions at 6 am PDT on Monday, May 18. All collected predictions will be posted to the Prediction Center's Data Archive the...
END OF SERVER DRY RUN; STAGE2 OF CASP-COVID; START OF CASP14 Dear CASPers, We are finishing testing CASP14 servers today and will be switching our main attention to the CASP-covid project in the next 4 days. If you still want to register a server for CASP14, ... Protein Structure Prediction Center Sponsored by the US National Institute of General Medical Sciences(NIH/NIGMS)
Please address any questions or queries to: casp@predictioncenter.org © 2007-2020, University of California, DavisDetails
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