Andriy Kryshtafovych

发表

Critical assessment of methods of protein structure prediction—Round VIII

B. Rost, A. Tramontano, K. Fidelis, 2009, Proteins.

Critical assessment of methods of protein structure prediction (CASP)—round IX

A. Tramontano, K. Fidelis, J. Moult, 2011, Proteins.

Evaluation of residue–residue contact predictions in CASP9

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2011, Proteins.

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

A. Tramontano, K. Fidelis, J. Moult, 2016, Proteins.

Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences

John A Tainer, Jose M. Duarte, Krzysztof Fidelis, 2019, Proteins.

Evaluation of residue–residue contact prediction in CASP10

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2014, Proteins.

Assessment of CASP11 contact‐assisted predictions

N. Grishin, L. Kinch, Andriy Kryshtafovych, 2016, Proteins.

New encouraging developments in contact prediction: Assessment of the CASP11 results

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2016, Proteins.

Discovering regulatory binding-site modules using rule-based learning.

K. Fidelis, J. Komorowski, Andriy Kryshtafovych, 2005, Genome research.

Critical assessment of methods of protein structure prediction (CASP)—Round XII

A. Tramontano, K. Fidelis, J. Moult, 2018, Proteins.

Protein structure prediction and model quality assessment.

K. Fidelis, Andriy Kryshtafovych, A. Kryshtafovych, 2009, Drug discovery today.

Generalized modeling of enzyme–ligand interactions using proteochemometrics and local protein substructures

K. Fidelis, P. Prusis, J. Komorowski, 2006, Proteins.

Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme‐Ligand Space.

K. Fidelis, G. Kleywegt, J. Wikberg, 2009 .

Evaluation of model refinement in CASP13

Randy J Read, Andriy Kryshtafovych, Massimo D Sammito, 2019, Proteins.

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

Torsten Schwede, Krzysztof Fidelis, Andriy Kryshtafovych, 2019, Proteins.

Local descriptors of protein structure: A systematic analysis of the sequence‐structure relationship in proteins using short‐ and long‐range interactions

Krzysztof Fidelis, Andriy Kryshtafovych, Torgeir R Hvidsten, 2009, Proteins.

Evaluation of disorder predictions in CASP9

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2011, Proteins.

Evaluation of model quality predictions in CASP9

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2011, Proteins.

CASP11 statistics and the prediction center evaluation system

Krzysztof Fidelis, Andriy Kryshtafovych, Bohdan Monastyrskyy, 2016, Proteins.

Protein structure prediction assisted with sparse NMR data in CASP13

David A. Snyder, C. Sander, Gaohua Liu, 2019, Proteins.

Title : Assessment of model accuracy estimations in CASP 12 Short title : Model accuracy assessment

A. Tramontano, K. Fidelis, Andriy Kryshtafovych, 2017 .

Target highlights in CASP13: Experimental target structures through the eyes of their authors

K. Fidelis, G. Phillips, J. Moult, 2019, Proteins.

Assessment of protein assembly prediction in CASP13

Jose M. Duarte, Dmytro Guzenko, Andriy Kryshtafovych, 2019, Proteins.

Target highlights from the first post‐PSI CASP experiment (CASP12, May–August 2016)

M. Nardini, K. Fidelis, J. Moult, 2018, Proteins.

Assessment of predictions in the model quality assessment category

Anna Tramontano, Domenico Cozzetto, Andriy Kryshtafovych, 2007, Proteins.

Target highlights in CASP14: Analysis of models by structure providers

K. Fidelis, J. Moult, J. Tainer, 2021, Proteins.

Critical assessment of methods of protein structure prediction (CASP)—Round XIV

K. Fidelis, J. Moult, Andriy Kryshtafovych, 2021, Proteins.

Evaluation of free modeling targets in CASP11 and ROLL

Lisa N Kinch, Nick V Grishin, Andriy Kryshtafovych, 2016, Proteins.

Evaluation of template‐based models in CASP8 with standard measures

Burkhard Rost, Anna Tramontano, Domenico Cozzetto, 2009, Proteins.

Assessing the accuracy of contact and distance predictions in CASP14

Andriy Kryshtafovych, A. Valencia, E. Milanetti, 2021, Proteins.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Christopher J. Williams, Soon Wen Hoh, Colin M. Palmer, 2021, Nature Methods.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

Genki Terashi, Daisuke Kihara, Grigore D. Pintilie, 2020, bioRxiv.

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

Wah Chiu, Andriy Kryshtafovych, Bohdan Monastyrskyy, 2019, Proteins.

Evaluation system and web infrastructure for the second cryo-EM model challenge.

Wah Chiu, Andriy Kryshtafovych, Paul D Adams, 2018, Journal of structural biology.

Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge

W. Chiu, P. Adams, Andriy Kryshtafovych, 2018, Data in brief.

Outcome of a workshop on applications of protein models in biomedical research.

Roland L Dunbrack, Roland L. Dunbrack, Andrej Sali, 2009, Structure.

Critical assessment of methods of protein structure prediction—Round VII

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2007, Proteins.

Progress over the first decade of CASP experiments

Ceslovas Venclovas, Krzysztof Fidelis, Andriy Kryshtafovych, 2005, Proteins.

Evaluation of template‐based modeling in CASP13

Randy J Read, Andriy Kryshtafovych, Tristan I Croll, 2019, Proteins.

Some of the most interesting CASP11 targets through the eyes of their authors

Victor Seguritan, Thomas S. Peat, Forest Rohwer, 2015, Proteins.

Evaluation of the template‐based modeling in CASP12

Anna Tramontano, Torsten Schwede, Krzysztof Fidelis, 2018, Proteins.

Critical assessment of methods of protein structure prediction (CASP) — round x

Anna Tramontano, Torsten Schwede, Krzysztof Fidelis, 2014, Proteins.

Assessment of protein disorder region predictions in CASP10

Anna Tramontano, Krzysztof Fidelis, Andriy Kryshtafovych, 2014, Proteins.

Assessing the accuracy of contact predictions in CASP13

Rojan Shrestha, Nelson Gil, Krzysztof Fidelis, 2019, Proteins.

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age

Andriy Kryshtafovych, Bohdan Monastyrskyy, Joerg Schaarschmidt, 2017, Proteins.

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

Marco Biasini, Victor Seguritan, Forest Rohwer, 2014, Proteins.

Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges

Chaok Seok, Andriy Kryshtafovych, Jonghun Won, 2021, Proteins.

Computational models in the service of X‐ray and cryo‐electron microscopy structure determination

J. Moult, Andriy Kryshtafovych, A. Lupas, 2021, Proteins.

Computational models in the service of X-ray and cryo-EM structure determination

Andrei N. Lupas, Andriy Kryshtafovych, John Moult, 2021 .

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Adam Liwo, Juri Rappsilber, J Eduardo Fajardo, 2019, Proteins.

Petascale Homology Search for Structure Prediction

Eli Levy Karin, Andriy Kryshtafovych, R. Chikhi, 2023, bioRxiv.

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

Protein Model Database

Andriy Kryshtafovych, Krzysztof Fidelis, Pawel Daniluk, 2005 .

Comparative analysis of methods for evaluation of protein models against native structures

Kliment Olechnovic, Ceslovas Venclovas, Andriy Kryshtafovych, 2018, Bioinform..

CASP10 results compared to those of previous CASP experiments

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2014, Proteins.

Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

Č. Venclovas, K. Fidelis, J. Moult, 2021, Proteins.

New prediction categories in CASP15

K. Fidelis, J. Moult, Rhiju Das, 2023, Proteins.

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

Mark J van Raaij, Liang Tong, Torsten Schwede, 2011, Proteins.

Assessment of the CASP14 assembly predictions

Andriy Kryshtafovych, E. Karaca, A. Kryshtafovych, 2021, Proteins.

Evaluation of model refinement in CASP14

Filomeno Sánchez Rodríguez, Andriy Kryshtafovych, D. Rigden, 2021, Proteins.

Protein target highlights in CASP15: Analysis of models by structure providers

Peter L. Freddolino, Mitchell D. Miller, K. Fidelis, 2023, Proteins.

Assessment of the assessment: Evaluation of the model quality estimates in CASP10

Anna Tramontano, Alessandro Barbato, Torsten Schwede, 2014, Proteins.

FliD , the flagellar cap protein from Pseudomonas aeruginosa PAO 1 ( CASP : T 0886 , Ts 886 , PDB : 5 FHY ) : Provided by

M. Nardini, K. Fidelis, J. Moult, 2017 .

Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts

Torgeir R. Hvidsten, Robin Andersson, Krzysztof Fidelis, 2009, Bioinform..

CASP13 target classification into tertiary structure prediction categories

Lisa N Kinch, Nick V Grishin, Andriy Kryshtafovych, 2019, Proteins.