Andriy Kryshtafovych

发表

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

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

Fold recognition using sequence fingerprints of protein local substructures

Jan Komorowski, Torgeir R. Hvidsten, Krzysztof Fidelis, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

CASP 11 target classification

R Dustin Schaeffer, Lisa N Kinch, Nick V Grishin, 2016, Proteins.

Using local gene expression similarities to discover regulatory binding site modules

Bartek Wilczynski, Jerzy Tiuryn, Jan Komorowski, 2006, BMC Bioinformatics.

Evaluation of the template‐based modeling in CASP12

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

CASP6 data processing and automatic evaluation at the protein structure prediction center

Maciej Milostan, Krzysztof Fidelis, Andriy Kryshtafovych, 2005, Proteins.

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.

New tools and expanded data analysis capabilities at the protein structure prediction center

Andreas Prlic, Maciej Milostan, Krzysztof Fidelis, 2007, Proteins.

Assessment of protein assembly prediction in CASP13

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

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning

Minkyung Baek, Chaok Seok, Andriy Kryshtafovych, 2019, Proteins.

Progress over the first decade of CASP experiments

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

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

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

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

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

CASP11 statistics and the prediction center evaluation system

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

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

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

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..

CASP10 results compared to those of previous CASP experiments

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

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.

A rule-based framework for gene regulation pathways discovery

Jan Komorowski, Torgeir R. Hvidsten, Krzysztof Fidelis, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Protein structure prediction center in CASP8

Krzysztof Fidelis, Andriy Kryshtafovych, Pawel Daniluk, 2009, Proteins.

Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11

Anna Tramontano, Alessandro Barbato, Torsten Schwede, 2016, 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.

A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins

Jan Komorowski, Torgeir R. Hvidsten, Krzysztof Fidelis, 2004, Bioinform..

Assessment of protein disorder region predictions in CASP10

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

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

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

Definition and classification of evaluation units for CASP10

Yuanpeng J Huang, Gaetano T Montelione, Chin-Hsien Tai, 2014, Proteins.

Small angle X‐ray scattering and cross‐linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy

Juri Rappsilber, John A Tainer, Adam Belsom, 2018, Proteins.

CASP: A Driving Force in Protein Structure Modeling

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2010 .

System for accepting server predictions in CASP6

Maciej Milostan, Krzysztof Fidelis, Andriy Kryshtafovych, 2005, Proteins.

CASP13 target classification into tertiary structure prediction categories

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

A tribute to Anna Tramontano (1957–2017)

Torsten Schwede, Krzysztof Fidelis, Andriy Kryshtafovych, 2018, Proteins.

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

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

Assessing the accuracy of contact predictions in CASP13

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

Evaluation of template‐based models in CASP8 with standard measures

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

Assessment of model accuracy estimations in CASP12

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

Protein Model Database

Andriy Kryshtafovych, Krzysztof Fidelis, Pawel Daniluk, 2005 .

Progress from CASP6 to CASP7

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2007, Proteins.

Evaluation of CASP8 model quality predictions

Anna Tramontano, Domenico Cozzetto, Andriy Kryshtafovych, 2009, Proteins.

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

Krzysztof Fidelis, Andriy Kryshtafovych, Bohdan Monastyrskyy, 2014, Proteins.

CASP8 results in context of previous experiments

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2009, Proteins.

Evaluation of free modeling targets in CASP11 and ROLL

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

Critical assessment of methods of protein structure prediction—Round VII

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

Assessment of protein assembly prediction in CASP12

Torsten Schwede, Jose M. Duarte, Andriy Kryshtafovych, 2018, Proteins.

Assessment of the model refinement category in CASP12

Francesco Luigi Gervasio, Giorgio Saladino, Andriy Kryshtafovych, 2018, Proteins.

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

Andriy Kryshtafovych, Bohdan Monastyrskyy, Matteo Dal Peraro, 2018, Proteins.

CASP9 results compared to those of previous casp experiments

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2011, Proteins.

Evaluation of template‐based modeling in CASP13

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

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

Jarl E. S. Wikberg, Gerard J. Kleywegt, Torgeir R. Hvidsten, 2008, J. Chem. Inf. Model..

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

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

Assessment of predictions in the model quality assessment category

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

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi‐automated metrics

Lisa N Kinch, Andriy Kryshtafovych, Bohdan Monastyrskyy, 2018, Proteins.

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

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

Author response for "Assessment of domain interactions in CASP14"

Nick V. Grishin, Andriy Kryshtafovych, R. Dustin Schaeffer, 2021 .

Evaluation of model refinement in CASP14

Adam Simpkin, Andriy Kryshtafovych, Daniel Rigden, 2021 .

Author response for "Assessment of protein model structure accuracy estimation in CASP14 : Old and new challenges"

Chaok Seok, Andriy Kryshtafovych, Jonghun Won, 2021 .

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

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

A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity

Jan Komorowski, Torgeir R. Hvidsten, Krzysztof Fidelis, 2009, PloS one.

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.

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.

CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge

Takeshi Kawabata, Haruki Nakamura, Genki Terashi, 2018 .

Evaluation of model quality predictions in CASP9

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

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.

Evaluation of residue–residue contact prediction in CASP10

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

Progress from CASP 6 to CASP 7

Krzysztof Fidelis, Andriy Kryshtafovych, John Moult, 2007 .

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.