Works matching IS 08873585 AND DT 2023 AND VI 91 AND IP 12

Results: 34

Cover Image, Volume 91, Issue 12.

Published in:

Proteins, 2023, v. 91, n. 12, p. C4, doi. 10.1002/prot.26640

By:

Das, Rhiju;
Kretsch, Rachael C.;
Simpkin, Adam J.;
Mulvaney, Thomas;
Pham, Phillip;
Rangan, Ramya;
Bu, Fan;
Keegan, Ronan M.;
Topf, Maya;
Rigden, Daniel J.;
Miao, Zhichao;
Westhof, Eric

Publication type:

Article

Cover Image, Volume 91, Issue 12.

Published in:

Proteins, 2023, v. 91, n. 12, p. C1, doi. 10.1002/prot.26639

By:

Ozden, Burcu;
Kryshtafovych, Andriy;
Karaca, Ezgi

Publication type:

Article

Issue Information ‐ Table of Content.

Published in:: Proteins, 2023, v. 91, n. 12, p. 1535, doi. 10.1002/prot.26379
Publication type:: Article

Integrating deep learning, threading alignments, and a multiMSA strategy for high-quality protein monomer and complex structure prediction in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1684, doi. 10.1002/prot.26585

By:

Wei Zheng;
Qiqige Wuyun;
Freddolino, Peter L.;
Yang Zhang

Publication type:

Article

Template-guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1829, doi. 10.1002/prot.26535

By:

Xianjin Xu;
Rui Duan;
Xiaoqin Zou

Publication type:

Article

Improved multimer prediction using massive sampling with AlphaFold in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1734, doi. 10.1002/prot.26562

By:

Wallner, Björn

Publication type:

Article

Assessment of the assessment—All about complexes.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1850, doi. 10.1002/prot.26612

By:

Studer, Gabriel;
Tauriello, Gerardo;
Schwede, Torsten

Publication type:

Article

Tertiary structure assessment at CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1616, doi. 10.1002/prot.26593

By:

Simpkin, Adam J.;
Mesdaghi, Shahram;
Rodríguez, Filomeno Sánchez;
Elliott, Luc;
Murphy, David L.;
Kryshtafovych, Andriy;
Keegan, Ronan M.;
Rigden, Daniel J.

Publication type:

Article

zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1837, doi. 10.1002/prot.26573

By:

Tao Shen;
Fuxu Liu;
Zechen Wang;
Jinyuan Sun;
Yifan Bu;
Jintao Meng;
Weihua Chen;
Keyi Yao;
Yuguang Mu;
Weifeng Li;
Guoping Zhao;
Sheng Wang;
Yanjie Wei;
Liangzhen Zheng

Publication type:

Article

RNA tertiary structure prediction using RNAComposer in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1790, doi. 10.1002/prot.26578

By:

Sarzynska, Joanna;
Popenda, Mariusz;
Antczak, Maciej;
Szachniuk, Marta

Publication type:

Article

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1889, doi. 10.1002/prot.26542

By:

Roy, Raj S.;
Jian Liu;
Giri, Nabin;
Zhiye Guo;
Jianlin Cheng

Publication type:

Article

Assessment of protein–ligand complexes in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1811, doi. 10.1002/prot.26601

By:

Robin, Xavier;
Studer, Gabriel;
Durairaj, Janani;
Eberhardt, Jerome;
Schwede, Torsten;
Walters, W. Patrick

Publication type:

Article

Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1704, doi. 10.1002/prot.26570

By:

Zhenling Peng;
Wenkai Wang;
Hong Wei;
Xiaoge Li;
Jianyi Yang

Publication type:

Article

The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1636, doi. 10.1002/prot.26598

By:

Ozden, Burcu;
Kryshtafovych, Andriy;
Karaca, Ezgi

Publication type:

Article

VoroIF-GNN: Voronoi tessellation-derived protein–protein interface assessment using a graph neural network.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1879, doi. 10.1002/prot.26554

By:

Olechnovič, Kliment;
Venclovas, Česlovas

Publication type:

Article

Prediction of protein assemblies by structure sampling followed by interface-focused scoring.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1724, doi. 10.1002/prot.26569

By:

Olechnovič, Kliment;
Valančauskas, Lukas;
Dapkūnas, Justas;
Venclovas, Česlovas

Publication type:

Article

Improving protein structure prediction with extended sequence similarity searches and deep-learning-based refinement in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1712, doi. 10.1002/prot.26551

By:

Toshiyuki Oda

Publication type:

Article

CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1935, doi. 10.1002/prot.26644

By:

Mulvaney, Thomas;
Kretsch, Rachael C.;
Elliott, Luc;
Beton, Joseph G.;
Kryshtafovych, Andriy;
Rigden, Daniel J.;
Das, Rhiju;
Topf, Maya

Publication type:

Article

Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1861, doi. 10.1002/prot.26564

By:

Jun Liu;
Dong Liu;
Guangxing He;
Guijun Zhang

Publication type:

Article

Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1779, doi. 10.1002/prot.26583

By:

Jun Li;
Sicheng Zhang;
Shi-Jie Chen

Publication type:

Article

Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1903, doi. 10.1002/prot.26584

By:

Kryshtafovych, Andriy;
Montelione, Gaetano T.;
Rigden, Daniel J.;
Mesdaghi, Shahram;
Karaca, Ezgi;
Moult, John

Publication type:

Article

Automated benchmarking of combined protein structure and ligand conformation prediction.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1912, doi. 10.1002/prot.26605

By:

Leemann, Michèle;
Sagasta, Ander;
Eberhardt, Jerome;
Schwede, Torsten;
Robin, Xavier;
Durairaj, Janani

Publication type:

Article

To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1558, doi. 10.1002/prot.26533

By:

Kryshtafovych, Andriy;
Rigden, Daniel J.

Publication type:

Article

New prediction categories in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1550, doi. 10.1002/prot.26515

By:

Kryshtafovych, Andriy;
Antczak, Maciej;
Szachniuk, Marta;
Zok, Tomasz;
Kretsch, Rachael C.;
Rangan, Ramya;
Pham, Phillip;
Das, Rhiju;
Robin, Xavier;
Studer, Gabriel;
Durairaj, Janani;
Eberhardt, Jerome;
Sweeney, Aaron;
Topf, Maya;
Schwede, Torsten;
Fidelis, Krzysztof;
Moult, John

Publication type:

Article

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

Published in:

Proteins, 2023, v. 91, n. 12, p. 1539, doi. 10.1002/prot.26617

By:

Kryshtafovych, Andriy;
Schwede, Torsten;
Topf, Maya;
Fidelis, Krzysztof;
Moult, John

Publication type:

Article

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1658, doi. 10.1002/prot.26609

By:

Lensink, Marc F.;
Brysbaert, Guillaume;
Raouraoua, Nessim;
Bates, Paul A.;
Giulini, Marco;
Honorato, Rodrigo V.;
van Noort, Charlotte;
Teixeira, Joao M. C.;
Bonvin, Alexandre M. J. J.;
Ren Kong;
Hang Shi;
Xufeng Lu;
Shan Chang;
Jian Liu;
Zhiye Guo;
Xiao Chen;
Morehead, Alex;
Roy, Raj S.;
Tianqi Wu;
Giri, Nabin

Publication type:

Article

RNA target highlights in CASP15: Evaluation of predicted models by structure providers.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1600, doi. 10.1002/prot.26550

By:

Kretsch, Rachael C.;
Andersen, Ebbe S.;
Bujnicki, Janusz M.;
Chiu, Wah;
Das, Rhiju;
Bingnan Luo;
Masquida, Benoît;
McRae, Ewan K. S.;
Schroeder, Griffin M.;
Zhaoming Su;
Wedekind, Joseph E.;
Lily Xu;
Kaiming Zhang;
Zheludev, Ivan N.;
Moult, John;
Kryshtafovych, Andriy

Publication type:

Article

Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1822, doi. 10.1002/prot.26587

By:

Kotelnikov, Sergei;
Ashizawa, Ryota;
Popov, Konstantin I.;
Khan, Omeir;
Ignatov, Mikhail;
Stan Xiaogang Li;
Hassan, Mosavverul;
Coutsias, Evangelos A.;
Poda, Gennady;
Padhorny, Dzmitry;
Tropsha, Alexander;
Vajda, Sandor;
Kozakov, Dima

Publication type:

Article

Estimation of model accuracy in CASP15 using the ModFOLDdock server.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1871, doi. 10.1002/prot.26532

By:

Edmunds, Nicholas S.;
Alharbi, Shuaa M. A.;
Genc, Ahmet G.;
Adiyaman, Recep;
McGuffin, Liam J.

Publication type:

Article

Assessment of three-dimensional RNA structure prediction in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1747, doi. 10.1002/prot.26602

By:

Das, Rhiju;
Kretsch, Rachael C.;
Simpkin, Adam J.;
Mulvaney, Thomas;
Pham, Phillip;
Rangan, Ramya;
Bu, Fan;
Keegan, Ronan M.;
Topf, Maya;
Rigden, Daniel J.;
Miao, Zhichao;
Westhof, Eric

Publication type:

Article

Critical assessment of protein intrinsic disorder prediction (CAID) - Results of round 2.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1925, doi. 10.1002/prot.26582

By:

Conte, Alessio Del;
Mehdiabadi, Mahta;
Bouhraoua, Adel;
Monzon, Alexander Miguel;
Tosatto, Silvio C. E.;
Piovesan, Damiano

Publication type:

Article

RNA tertiary structure modeling with BRiQ potential in CASP15.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1771, doi. 10.1002/prot.26574

By:

Ke Chen;
Yaoqi Zhou;
Sheng Wang;
Peng Xiong

Publication type:

Article

RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1800, doi. 10.1002/prot.26575

By:

Baulin, Eugene F.;
Mukherjee, Sunandan;
Moafinejad, S. Naeim;
Wirecki, Tomasz K.;
Badepally, Nagendar Goud;
Jaryani, Farhang;
Stefaniak, Filip;
Farsani, Masoud Amiri;
Ray, Angana;
de Moura, Tales Rocha;
Bujnicki, Janusz M.

Publication type:

Article

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

Published in:

Proteins, 2023, v. 91, n. 12, p. 1571, doi. 10.1002/prot.26545

By:

Alexander, Leila T.;
Durairaj, Janani;
Kryshtafovych, Andriy;
Abriata, Luciano A.;
Bayo, Yusupha;
Bhabha, Gira;
Breyton, Cécile;
Caulton, Simon G.;
Chen, James;
Degroux, Séraphine;
Ekiert, Damian C.;
Erlandsen, Benedikte S.;
Freddolino, Peter L.;
Gilzer, Dominic;
Greening, Chris;
Grimes, Jonathan M.;
Grinter, Rhys;
Gurusaran, Manickam;
Hartmann, Marcus D.;
Hitchman, Charlie J.

Publication type:

Article