Protein modeling, ligand-protein docking, and visualization by Lu, Bai Fang

“…This motivates us to develop a ligand-protein docking algorithm with emphasis on high performance.…”
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Protein-protein docking based on geometric complementarity by Liu, Hui

“…In our work, the “divide and conquer” scheme has been utilized for protein-protein docking, with an initial stage which focuses on generating a reasonable list of near-native candidate docking conformations, and a refinement step which aims to rank the hit within the first several positions by incorporating the protein flexibility into the docking procedure. …”
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Protein-protein docking with dynamic residue protonation states. by Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J Gray

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A Non-Redundant Benchmark for Symmetric Protein Docking by Yumeng Yan, Sheng-You Huang

“…In the present work, we develop a comprehensive and non-redundant benchmark for symmetric protein docking based on the structures in the Protein Data Bank (PDB). …”
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Exploring angular distance in protein-protein docking algorithms. by Thom Vreven, Howook Hwang, Zhiping Weng

“…We present a two-stage hybrid-resolution approach for rigid-body protein-protein docking. The first stage is carried out at low-resolution (15°) angular sampling. …”
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Sampling the conformation of protein surface residues for flexible protein docking by Amenta Nina, Hass Joel, Gu Shengyin, Francis-Lyon Patricia, Koehl Patrice

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Harnessing protein folding neural networks for peptide–protein docking by Tomer Tsaban, Julia K. Varga, Orly Avraham, Ziv Ben-Aharon, Alisa Khramushin, Ora Schueler-Furman

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PROTEIN-PROTEIN DOCKING REFINEMENT USING RESTRAINT MOLECULAR DYNAMICS SIMULATIONS by MARTIN ZACHARIAS

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Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. by William Sheffler, Erin C Yang, Quinton Dowling, Yang Hsia, Chelsea N Fries, Jenna Stanislaw, Mark D Langowski, Marisa Brandys, Zhe Li, Rebecca Skotheim, Andrew J Borst, Alena Khmelinskaia, Neil P King, David Baker

“…Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. …”
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MEGADOCK-on-Colab: an easy-to-use protein–protein docking tool on Google Colaboratory by Masahito Ohue

Subjects: “…Protein–protein docking…”
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AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking by Wisitponchai, Tanchanok, Shoombuatong, Watshara, Lee, Vannajan Sanghiran, Kitidee, Kuntida, Tayapiwatana, Chatchai

“…In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses. Conclusion: The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. …”

Accelerating the Screening of Small Peptide Ligands by Combining Peptide-Protein Docking and Machine Learning by Josep-Ramon Codina, Marcello Mascini, Emre Dikici, Sapna K. Deo, Sylvia Daunert

“…LightGBM was used to classify peptide-protein docking performance of the entire tetrapeptide library of 160,000 peptide ligands against four viral envelope proteins. …”
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A Point Cloud-Based Deep Learning Model for Protein Docking Decoys Evaluation by Ye Han, Simin Zhang, Fei He

Subjects: “…protein docking…”
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How ‘Protein-Docking’ Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids? by Francesca Tessaro, Leonardo Scapozza

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Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold by Francis Gaudreault, Jason Baardsnes, Yuliya Martynova, Aurore Dachon, Hervé Hogues, Christopher R. Corbeil, Enrico O. Purisima, Mélanie Arbour, Traian Sulea, Traian Sulea

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Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models. by Edrisse Chermak, Renato De Donato, Marc F Lensink, Andrea Petta, Luigi Serra, Vittorio Scarano, Luigi Cavallo, Romina Oliva

“…Correctly scoring protein-protein docking models to single out native-like ones is an open challenge. …”
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An Investigation of Three-Finger Toxin—nAChR Interactions through Rosetta Protein Docking by Alican Gulsevin, Jens Meiler

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Impacts of Biosynthesized Manganese Dioxide Nanoparticles on Antioxidant Capacity, Hematological Parameters, and Antioxidant Protein Docking in Broilers by Esraa S. Helbawi, S. A. Abd El-Latif, Mahmoud A. Toson, Artur Banach, Mohamed Mohany, Salim S. Al-Rejaie, Hamada Elwan

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Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations by Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Kolinski

“…Most of the protein–protein docking methods treat proteins as almost rigid objects. …”
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Improved Functionality of Integration-Deficient Lentiviral Vectors (IDLVs) by the Inclusion of IS₂ Protein Docks by Marina Cortijo-Gutiérrez, Sabina Sánchez-Hernández, María Tristán-Manzano, Noelia Maldonado-Pérez, Lourdes Lopez-Onieva, Pedro J. Real, Concha Herrera, Juan Antonio Marchal, Francisco Martin, Karim Benabdellah

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