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

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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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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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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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Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes by Uchikoga Nobuyuki, Hirokawa Takatsugu

“…Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. …”
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NPPD: A Protein-Protein Docking Scoring Function Based on Dyadic Differences in Networks of Hydrophobic and Hydrophilic Amino Acid Residues by Edward S. C. Shih, Ming-Jing Hwang

Subjects: “…protein-protein docking…”
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MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations by Yong Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant G. Honavar

Subjects: “…protein–protein docking…”
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Protein-protein docking studies on the sweet protein (neoculin) and the human sweet taste receptors T1R2 and T1R3 by Ahmad Khairudin, Nurul Bahiyah, Yousif, Ragheed Hussam

“…Therefore, in this work, a protein-protein docking study was performed between neoculin and the human sweet taste receptor T1R2 and T1R3. …”

Mapping the energy landscape of PROTAC-mediated protein-protein interactions by José A. Villegas, Tasneem M. Vaid, Michael E. Johnson, Terry W. Moore

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Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach by Priyanka Bhandu, Himanshu Verma, Baddipadige Raju, Gera Narendra, Shalki Choudhary, Manmeet Singh, Pankaj Kumar Singh, Om Silakari

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Deconvolution of the MBP-Bri2 Interaction by a Yeast Two Hybrid System and Synergy of the AlphaFold2 and High Ambiguity Driven Protein-Protein Docking by Evgeniya V. Smirnova, Tatiana V. Rakitina, George A. Saratov, Anna A. Kudriaeva, Alexey A. Belogurov

“…Since the spatial structures for both MBP and Bri2 were not known, we used computational methods of structural biology including an artificial intelligence system AlphaFold2 and high ambiguity driven protein-protein docking (HADDOCK 2.1) to gain a mechanistic explanation of the found protein-protein interaction and elucidate a possible structure of the complex of MBP with Bri23R peptide. …”
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Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection by Sonam Gupta, Prithvi Singh, Alvea Tasneem, Ahmad Almatroudi, Arshad Husain Rahmani, Ravins Dohare, Shama Parveen

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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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Molecular Interaction-Based Exploration of the Broad Spectrum Efficacy of a Bacillus thuringiensis Insecticidal Chimeric Protein, Cry1AcF by Maniraj Rathinam, Karthik Kesiraju, Shweta Singh, Vinutha Thimmegowda, Vandna Rai, Debasis Pattanayak, Rohini Sreevathsa

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A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase by Davide Doni, Marta Meggiolaro, Javier Santos, Gérard Audran, Sylvain R. A. Marque, Paola Costantini, Marco Bortolus, Donatella Carbonera

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Identification of Sortilin Alternatively Spliced Variants in Mouse 3T3L1 Adipocytes by Ashley Lui, Robert Sparks, Rekha Patel, Niketa A. Patel

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Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy by Serwa Ghasemi, Mohammad Mahdavi, Majid Maleki, Iman Salahshourifar, Samira Kalayinia

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