Docking Benchmark 5.5

Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2. ... Table: Protein-Protein Docking ...

Docking Benchmark Version 5 and Affinity Benchmark Version 2

We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks.

haddocking/BM5-clean: Docking benchmark 5 - GitHub

Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2.

a non-redundant structure benchmark dataset for antibody–antigen ...

In this work, we first reviewed previously developed ABAG-docking datasets, including Benchmark versions 4.0, 5.0 and 5.5, in terms of dataset ...

Antibody Docking and Affinity Benchmark - GitHub

This repository contains the antibody-antigen test cases, with unbound and bound structures, for Docking Benchmark 5.5.

An Expanded Benchmark for Antibody-Antigen Docking and Affinity ...

Docking Benchmark 5.5, which includes the antibody benchmark cases described here, is available at: https://zlab.umassmed.edu/benchmark/benchmark5.5.html.

Advancing membrane-associated protein docking with improved ...

(DB 5.5) for soluble protein complexes, which ... Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of. 349.

Updates to the Integrated Protein-Protein Interaction Benchmarks

The current study analyzes the secondary shell hotspots in the 94 protein-protein complexes newly curated from the Docking Benchmark 5.5 37, 38 . We observe ...

Docking Benchmark Group - TDC - Therapeutics Data Commons

This benchmark evaluates generated molecules against their affinity to the target protein (ie, quantified through docking scores).

a non-redundant structure benchmark dataset for antibody–antigen ...

Compared with Docking Benchmark 5.5, we have added 112 cases, including 14 single-domain antibody (sdAb) cases and 98 monoclonal antibody (mAb) cases, and ...

Reliable protein-protein docking with AlphaFold, Rosetta, and ... - eLife

Further, all of these DL docking tools have low success rates on unbound docking targets such as those in Docking Benchmark 5.5. In this ...

A Protein-Protein Docking Benchmark | Request PDF - ResearchGate

Two protein-protein docking datasets, Docking Benchmark 5.5 (DB5.5) [41] [42] [43][44][45] and Database of Interacting Protein Structures (DIPS) 46 , are ...

PDBBind Benchmark (Blind Docking) - Papers With Code

Blind Docking on PDBBind. Leaderboard; Dataset. View. Top-1 RMSD (%<2), Top-1 RMSD ... 5.5, 6.2. EquiBind: Geometric Deep Learning for Drug Binding Structure ...

Benchmark - ZDOCK: Protein Docking - ZLab

TCR Docking Benchmark: Includes 20 test cases of T cell receptors binding peptide/major histocompatibility complexes. Available here. Protein-Protein Docking:.

Benchmarking AlphaFold for protein complex modeling reveals ...

A test set of heterodimeric protein complexes was obtained from Protein–Protein Docking Benchmark 5.5 (BM5.5). ... BM5.5 is a set of structures of ...

Unified Sampling and Ranking for Protein Docking with DFMDock

Benchmark 5.5 test set. In successful decoy cases, the DFMDock ... Updates to the integrated protein–protein interaction benchmarks: docking ...

Quality Assessment of Protein Docking Models Based on Graph ...

The test samples were collected from Protein-Protein Docking Benchmark 5.5, which was updated in 2020 when DOVE and iScore were published. The ...

DockGame: Cooperative Games for Multimeric Rigid Protein Docking

... Docking Benchmark 5.5 (DB5.5) dataset, DockGame has much faster runtimes than traditional docking methods, can generate multiple plausible assembly ...

Biology+AI Daily on X: "Unified Sampling and Ranking for Protein ...

3/ In tests, DFMDock outperformed DiffDock-PP on the Docking Benchmark 5.5 (DB5.5) dataset. It achieved a sampling success rate of 44%, a ...

CABS-dock: server for protein-peptide docking

Benchmark set. CABS-dock performance for 103 bound cases and 68 unbound cases (listed in rows) in 3 independent prediction runs (shown in separate ...