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# PROTEINS: Structure, Function, and Bioinformatics | Protein Science Journal | Wiley Online Journal

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Proteins: Structure, Function, and Bioinformatics
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Proteins: Structure, Function, and Bioinformatics: Volume 94, Issue 1
Special issue: CASP16: Critical Assessment of methods for Structure Prediction, 16th round
Pages: C1-C4, 1-459
January 2026
Guest Editor(s):
John Moult
Andriy Kryshtafovych
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COVER IMAGE
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Cover Image, Volume 94, Issue 1
Andriy Kryshtafovych,  Torsten Schwede,  Maya Topf,  Krzysztof Fidelis,  John Moult
Page: C1 First Published: 29 December 2025

Obverse Cover 1: The cover image is based on the article Progress and bottlenecks for deep learning in computational structure biology: CASP round XVI by Andriy Kryshtafovych et al., https://doi.org/10.1002/prot.70076

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ADDITIONAL COVER
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Cover Image, Volume 94, Issue 1
Andriy Kryshtafovych,  Maciej Milostan,  Marc F. Lensink,  Sameer Velankar,  Alexandre M. J. J. Bonvin,  John Moult,  Krzysztof Fidelis
Page: C2 First Published: 29 December 2025

Obverse Cover 2: The cover image is based on the article Updates to the CASP infrastructure in 2024 by Andriy Kryshtafovych et al., https://doi.org/10.1002/prot.70042.

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Cover Image, Volume 94, Issue 1
Mahta Mehdiabadi,  Alessio Del Conte,  Maria Victoria Nugnes,  Maria Cristina Aspromonte,  Silvio C. E. Tosatto,  Damiano Piovesan
Page: C3 First Published: 29 December 2025

Reverse Cover 2: The cover image is based on the article Critical Assessment of Protein Intrinsic Disorder Round 3 - Predicting Disorder in the Era of Protein Language Models by Mahta Medihabadi et al., https://doi.org/10.1002/prot.70045.

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Cover Image, Volume 94, Issue 1
Allen C. McBride,  Feng Yu,  Edward H. Cheng,  Aulane Mpouli,  Aimee C. Soe,  Michal Hammel,  Gaetano T. Montelione,  Terrence G. Oas,  Susan E. Tsutakawa,  Bruce R. Donald
Page: C4 First Published: 29 December 2025

Reverse Cover 1: The cover image is based on the article Predicting pose distribution of protein domains connected by flexible linkers is an unsolved problem by Bruce Donald et al., https://doi.org/10.1002/prot.70062.

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ISSUE INFORMATION
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Issue Information - Table of Content
Pages: 1-3 First Published: 29 December 2025
First Page
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RESEARCH ARTICLE
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Progress and Bottlenecks for Deep Learning in Computational Structure Biology: CASP Round XVI
Andriy Kryshtafovych,  Torsten Schwede,  Maya Topf,  Krzysztof Fidelis,  John Moult
Pages: 5-14 First Published: 03 November 2025
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Updates to the CASP Infrastructure in 2024
Andriy Kryshtafovych,  Maciej Milostan,  Marc F. Lensink,  Sameer Velankar,  Alexandre M. J. J. Bonvin,  John Moult,  Krzysztof Fidelis
Pages: 15-24 First Published: 01 September 2025
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Protein Target Highlights in CASP16: Insights From the Structure Providers
Leila T. Alexander,  Océane M. Follonier,  Andriy Kryshtafovych,  Kim Abesamis,  Sabrina Bibi-Triki,  Henry G. Box,  Cécile Breyton,  Françoise Bringel,  Loic Carrique,  Alessio d'Acapito,  Gang Dong,  Rebecca DuBois,  Deborah Fass,  Juliana Martinez Fiesco,  Daniel R. Fox,  Jonathan M. Grimes,  Rhys Grinter,  Matthew Jenkins,  Roman Kamyshinsky,  Jeremy R. Keown,  Gerald Lackner,  Michael Lammers,  Shiheng Liu,  Andrew L. Lovering,  Tomas Malinauskas,  Benoît Masquida,  Gottfried J. Palm,  Christian Siebold,  Tiantian Su,  Ping Zhang,  Z. Hong Zhou,  Krzysztof Fidelis,  Maya Topf,  John Moult,  Torsten Schwede
Pages: 25-50 First Published: 09 October 2025
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Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers
Rachael C. Kretsch,  Reinhard Albrecht,  Ebbe S. Andersen,  Hsuan-Ai Chen,  Wah Chiu,  Rhiju Das,  Jeanine G. Gezelle,  Marcus D. Hartmann,  Claudia Höbartner,  Yimin Hu,  Shekhar Jadhav,  Philip E. Johnson,  Christopher P. Jones,  Deepak Koirala,  Emil L. Kristoffersen,  Eric Largy,  Anna Lewicka,  Cameron D. Mackereth,  Marco Marcia,  Michela Nigro,  Manju Ojha,  Joseph A. Piccirilli,  Phoebe A. Rice,  Heewhan Shin,  Anna-Lena Steckelberg,  Zhaoming Su,  Yoshita Srivastava,  Liu Wang,  Yuan Wu,  Jiahao Xie,  Nikolaj H. Zwergius,  John Moult,  Andriy Kryshtafovych
Pages: 51-78 First Published: 04 September 2025
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The CASP 16 Experimental Protein–Ligand Datasets
Andreas Tosstorff,  Markus G. Rudolph,  Jörg Benz,  Bernd Kuhn,  Christian Kramer,  May Sharpe,  Chia-Ying Huang,  Alexander Metz,  Julien Hazemann,  Daniel Ritz,  Aengus Mac Sweeney,  Michael K. Gilson
Pages: 79-85 First Published: 03 October 2025
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CASP16 Protein Monomer Structure Prediction Assessment
Rongqing Yuan,  Jing Zhang,  Andriy Kryshtafovych,  R. Dustin Schaeffer,  Jian Zhou,  Qian Cong,  Nick V. Grishin
Pages: 86-105 First Published: 17 August 2025
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Assessment of Protein Complex Predictions in CASP16: Are We Making Progress?
Jing Zhang,  Rongqing Yuan,  Andriy Kryshtafovych,  Jimin Pei,  Rachael C. Kretsch,  R. Dustin Schaeffer,  Jian Zhou,  Rhiju Das,  Nick V. Grishin,  Qian Cong
Pages: 106-130 First Published: 31 October 2025
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Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16
Jian Liu,  Pawan Neupane,  Jianlin Cheng
Pages: 131-141 First Published: 02 June 2025
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Accurate Biomolecular Structure Prediction in CASP16 With Optimized Inputs to State-Of-The-Art Predictors
Wenkai Wang,  Yuxian Luo,  Zhenling Peng,  Jianyi Yang
Pages: 142-153 First Published: 05 August 2025
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AlphaFold3 at CASP16
Arne Elofsson
Pages: 154-166 First Published: 25 August 2025
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Structure Modeling Protocols for Protein Multimer and RNA in CASP16 With Enhanced MSAs, Model Ranking, and Deep Learning
Yuki Kagaya,  Tsukasa Nakamura,  Jacob Verburgt,  Anika Jain,  Genki Terashi,  Pranav Punuru,  Emilia Tugolukova,  Joon Hong Park,  Anouka Saha,  David Huang,  Daisuke Kihara
Pages: 167-182 First Published: 01 August 2025
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Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16
Ryota Ashizawa,  Sergei Kotelnikov,  Omeir Khan,  Stan Xiaogang Li,  Ernest Glukhov,  Xin Cao,  Maria Lazou,  Ayse Bekar-Cesaretli,  Derara Hailegeorgis,  Veranika Averkava,  Yimin Zhu,  George Jones,  Hao Yu,  Dmytro Kalitin,  Darya Stepanenko,  Kushal Koirala,  Taras Patsahan,  Dmitri Beglov,  Mark Lukin,  Diane Joseph-McCarthy,  Carlos Simmerling,  Alexander Tropsha,  Evangelos Coutsias,  Ken A. Dill,  Dzmitry Padhorny,  Sandor Vajda,  Dima Kozakov
Pages: 183-191 First Published: 20 October 2025
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Assessment of Nucleic Acid Structure Prediction in CASP16
Rachael C. Kretsch,  Alissa M. Hummer,  Shujun He,  Rongqing Yuan,  Jing Zhang,  Thomas Karagianes,  Qian Cong,  Andriy Kryshtafovych,  Rhiju Das
Pages: 192-217 First Published: 30 October 2025
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The RNA-Puzzles Assessments of RNA-Only Targets in CASP16
Eric Westhof,  Hao Sun,  Fan Bu,  Zhichao Miao
Pages: 218-229 First Published: 03 October 2025
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Enhancing RNA 3D Structure Prediction: A Hybrid Approach Combining Expert Knowledge and Computational Tools in CASP16
Bowen Xiao,  Yaohuang Shi,  Lin Huang
Pages: 230-238 First Published: 08 August 2025
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