Uni-FEP-Benchmarks

Overview

Uni-FEP-Benchmarks is a benchmark dataset designed to systematically evaluate Uni-FEP, a free energy perturbation (FEP) method for accurate and efficient binding free energy calculations. This repository provides computational results across diverse protein-ligand systems and complex chemical transformations, facilitating validation and optimization of the Uni-FEP methodology.

We have summarized the background, methods, and key findings of Uni-FEP-Benchmarks in the following preprint: Breaking Barriers in FEP Benchmarking: A Large-Scale Dataset Reflecting Real-World Drug Discovery Challenges.

Objectives

By compiling well-structured benchmark cases, this repository aims to:

1. Improve the stability of Uni-FEP

   • Through extensive testing across various systems, we aim to identify potential weaknesses in Uni-FEP and refine its robustness.

2. Establish standardized test data for tracking performance changes

   • By maintaining a structured benchmark dataset, we can systematically analyze the impact of each Uni-FEP update on computational accuracy.

3. Reduce the cost of FEP adoption for users

   • This repository is designed as a long-term project. Over time, as more benchmark cases are added, users may directly request pre-constructed systems from this dataset, allowing them to focus solely on predicting new compounds without having to reconstruct the entire system.

FEP Open Challenge

We are excited to announce the FEP Open Challenge an initiative aimed at validating the accuracy and stability of Uni-FEP through community participation. Researchers are invited to submit their own test cases using publicly available or published datasets. Our team will perform the FEP calculations on the submitted data and return the results, helping to dispel any doubts about Uni-FEP's performance.

Key points of the challenge include:

• Data-Driven Validation: Submit your test case (including a protein structure, reference ligand, and dataset file), and our team will evaluate it to verify Uni-FEPs precision.
• Public Benchmarking: All validated test cases and their results will be shared openly in the Uni-FEP-Benchmarks repository under the Apache 2.0 license, contributing to a transparent and high-quality benchmark dataset.
• Reward Policy: Publicly compare Uni-FEP with another commercial FEP tool under identical conditions using supporting evidence (e.g., via a preprint, blog, or journal article) to earn *a $50 Amazon Gift Cardwith **an additional $50 awarded upon verification if the other tool is shown to significantly outperform Uni-FEP.
  _{*Subject to validation}
  
• Participation Guidelines: To ensure fairness, each individual may only have one active submission at a time. Also, cases sourced from ChEMBL or BindingDB may be avoided during our review process.

For more details, please refer to our FEP Open Challenge introduction.

Summary of Benchmark Results

Total Systems: 437
Total Ligands: 8206 | Series | Target | N_Ligands | RMSE (kcal/mol) | R | Kendall's tau | Description | |---|---|---|---|---|---|---| | ChEMBL | ADK | 12 | 1.59 | 0.28 | 0.36 | CHEMBL642224 | | ChEMBL | ADK | 31 | 1.77 | 0.47 | 0.43 | CHEMBL642225 | | ChEMBL | ADK | 27 | 1.48 | 0.48 | 0.41 | CHEMBL643547 | | ChEMBL | AHCY | 14 | 1.34 | 0.23 | 0.30 | CHEMBL3294635 | | ChEMBL | AKR1C3 | 11 | 0.90 | 0.59 | 0.67 | CHEMBL4428988 | | ChEMBL | ALDH2 | 9 | 1.01 | 0.30 | 0.65 | CHEMBL3130565 | | ChEMBL | ALDH2 | 12 | 1.23 | 0.26 | 0.43 | CHEMBL641008 | | ChEMBL | AMPD2 | 14 | 1.36 | 0.54 | 0.46 | CHEMBL5240593 | | ChEMBL | AR | 25 | 1.39 | 0.36 | 0.40 | CHEMBL4411915 | | ChEMBL | AR | 9 | 1.37 | 0.31 | 0.28 | CHEMBL896869 | | ChEMBL | AURKA | 30 | 0.80 | 0.32 | 0.15 | CHEMBL1656337 | | ChEMBL | AURKA | 7 | 1.12 | 0.79 | 0.59 | CHEMBL2382841 | | ChEMBL | AURKA | 10 | 1.49 | 0.54 | 0.63 | CHEMBL912713 | | ChEMBL | BACE1 | 9 | 0.79 | 0.57 | 0.83 | CHEMBL2015090 | | ChEMBL | BACE1 | 13 | 1.71 | 0.25 | 0.38 | CHEMBL2155063 | | ChEMBL | BACE1 | 10 | 0.96 | 0.66 | 0.73 | CHEMBL2182237 | | ChEMBL | BACE1 | 9 | 1.23 | 0.54 | 0.50 | CHEMBL2183861 | | ChEMBL | BACE1 | 23 | 0.85 | 0.33 | 0.39 | CHEMBL2185271 | | ChEMBL | BACE1 | 10 | 0.96 | 0.89 | 0.91 | CHEMBL2352381 | | ChEMBL | BACE1 | 36 | 0.89 | 0.22 | 0.32 | CHEMBL2353183 | | ChEMBL | BACE1 | 17 | 1.38 | 0.25 | 0.29 | CHEMBL2384472 | | ChEMBL | BACE1 | 23 | 1.11 | 0.19 | 0.34 | CHEMBL2404725 | | ChEMBL | BACE1 | 15 | 1.29 | 0.58 | 0.73 | CHEMBL3635177 | | ChEMBL | BACE1 | 19 | 0.94 | 0.51 | 0.40 | CHEMBL3801550 | | ChEMBL | BACE1 | 12 | 1.35 | 0.33 | 0.43 | CHEMBL3868309 | | ChEMBL | BACE1 | 15 | 1.45 | 0.20 | 0.13 | CHEMBL3888552 | | ChEMBL | BACE1 | 13 | 0.61 | 0.60 | 0.52 | CHEMBL5054671 | | ChEMBL | BACE1 | 16 | 0.65 | 0.51 | 0.72 | CHEMBL5055929 | | ChEMBL | BCAT2 | 24 | 1.82 | 0.34 | 0.53 | CHEMBL3812805 | | ChEMBL | BCL2L1 | 16 | 0.69 | 0.61 | 0.70 | CHEMBL859053 | | ChEMBL | BRAF | 34 | 1.99 | 0.43 | 0.49 | CHEMBL1008210 | | ChEMBL | BRAF | 36 | 1.34 | 0.43 | 0.45 | CHEMBL4841804 | | ChEMBL | BRD2 | 26 | 0.88 | 0.75 | 0.30 | CHEMBL3382827 | | ChEMBL | BRD4 | 12 | 0.48 | 0.77 | 0.34 | CHEMBL2183681 | | ChEMBL | BRD4 | 18 | 1.20 | 0.47 | 0.37 | CHEMBL2433086 | | ChEMBL | BRD4 | 13 | 0.55 | 0.89 | 0.53 | CHEMBL2433591 | | ChEMBL | BRD4 | 26 | 0.68 | 0.50 | 0.60 | CHEMBL3414207 | | ChEMBL | BRD4 | 109 | 0.71 | 0.47 | 0.52 | CHEMBL3706176 | | ChEMBL | BRD4 | 29 | 1.08 | 0.63 | 0.57 | CHEMBL4020217 | | ChEMBL | BRD4 | 18 | 1.26 | 0.49 | 0.32 | CHEMBL4038392 | | ChEMBL | BRD4 | 15 | 1.11 | 0.28 | 0.31 | CHEMBL4193809 | | ChEMBL | BRD4 | 21 | 1.16 | 0.29 | 0.31 | CHEMBL4200424 | | ChEMBL | BRD4 | 31 | 1.25 | 0.90 | 0.85 | CHEMBL4223756 | | ChEMBL | BRD4 | 28 | 1.18 | 0.26 | 0.22 | CHEMBL4308744 | | ChEMBL | BRD4 | 25 | 0.73 | 0.36 | 0.45 | CHEMBL4310223 | | ChEMBL | BRD4 | 10 | 0.30 | 0.86 | 0.82 | CHEMBL4716982 | | ChEMBL | BRD4 | 24 | 0.66 | 0.40 | 0.53 | CHEMBL5037307 | | ChEMBL | BRD4 | 26 | 0.89 | 0.47 | 0.50 | CHEMBL5044553 | | ChEMBL | BRD4 | 36 | 0.76 | 0.49 | 0.50 | CHEMBL5137805 | | ChEMBL | BRDT | 17 | 0.51 | 0.61 | 0.51 | CHEMBL4200426 | | ChEMBL | BRPF1 | 17 | 0.65 | 0.60 | 0.62 | CHEMBL3385101 | | ChEMBL | BTK | 14 | 1.50 | 0.80 | 0.69 | CHEMBL3375466 | | ChEMBL | BTK | 30 | 0.79 | 0.59 | 0.43 | CHEMBL3407032 | | ChEMBL | BTK | 18 | 1.66 | 0.65 | 0.59 | CHEMBL4057948 | | ChEMBL | BTK | 24 | 0.86 | 0.57 | 0.56 | CHEMBL4201924 | | ChEMBL | BTK | 15 | 0.43 | 0.96 | 0.89 | CHEMBL5031679 | | ChEMBL | CALCRL | 30 | 0.81 | 0.47 | 0.47 | CHEMBL1772121 | | ChEMBL | CAMKK1 | 16 | 1.87 | 0.18 | 0.23 | CHEMBL4827617 | | ChEMBL | CDC7 | 27 | 1.43 | 0.26 | 0.32 | CHEMBL944978 | | ChEMBL | CDK2 | 18 | 1.05 | 0.39 | 0.47 | CHEMBL1002021 | | ChEMBL | CDK2 | 16 | 1.36 | 0.36 | 0.33 | CHEMBL1119481 | | ChEMBL | CDK2 | 12 | 1.21 | 0.37 | 0.21 | CHEMBL2013356 | | ChEMBL | CDK2 | 20 | 1.79 | 0.89 | 0.66 | CHEMBL2166172 | | ChEMBL | CDK2 | 18 | 1.26 | 0.54 | 0.56 | CHEMBL3101312 | | ChEMBL | CDK2 | 14 | 1.57 | 0.62 | 0.63 | CHEMBL3101313 | | ChEMBL | CDK2 | 25 | 0.65 | 0.59 | 0.52 | CHEMBL658939 | | ChEMBL | CDK2 | 13 | 1.83 | 0.30 | 0.30 | CHEMBL661124 | | ChEMBL | CDK2 | 9 | 1.40 | 0.62 | 0.83 | CHEMBL661127 | | ChEMBL | CDK2 | 20 | 0.79 | 0.74 | 0.64 | CHEMBL908827 | | ChEMBL | CDK2 | 17 | 1.98 | 0.42 | 0.35 | CHEMBL971698 | | ChEMBL | CDK2 | 21 | 0.80 | 0.22 | 0.39 | CHEMBL992478 | | ChEMBL | CHEK1 | 31 | 1.91 | 0.63 | 0.47 | CHEMBL2014248 | | ChEMBL | CHEK1 | 25 | 1.41 | 0.52 | 0.44 | CHEMBL2014579 | | ChEMBL | CHEK1 | 8 | 1.67 | 0.30 | 0.40 | CHEMBL3381275 | | ChEMBL | CHEK1 | 31 | 1.17 | 0.29 | 0.52 | CHEMBL894121 | | ChEMBL | CHKA | 16 | 1.84 | 0.24 | 0.49 | CHEMBL3769127 | | ChEMBL | CHKA | 17 | 1.54 | 0.33 | 0.48 | CHEMBL3769133 | | ChEMBL | CMA1 | 9 | 0.90 | 0.67 | 0.50 | CHEMBL4182330 | | ChEMBL | CNR2 | 22 | 1.60 | 0.59 | 0.55 | CHEMBL921109 | | ChEMBL | CREBBP | 12 | 0.56 | 0.91 | 0.82 | CHEMBL3817157 | | ChEMBL | CREBBP | 18 | 0.70 | 0.59 | 0.50 | CHEMBL4058600 | | ChEMBL | CREBBP | 34 | 0.71 | 0.75 | 0.53 | CHEMBL4186385 | | ChEMBL | CSF1R | 25 | 1.54 | 0.42 | 0.44 | CHEMBL951197 | | ChEMBL | CSNK1D | 13 | 1.48 | 0.47 | 0.50 | CHEMBL2211470 | | ChEMBL | CTSS | 9 | 1.31 | 0.25 | 0.44 | CHEMBL1212307 | | ChEMBL | CYP1A1 | 9 | 0.75 | 0.18 | 0.44 | CHEMBL4311586 | | ChEMBL | DDR1 | 18 | 1.06 | 0.78 | 0.56 | CHEMBL4151608 | | ChEMBL | DHFR | 22 | 1.06 | 0.58 | 0.50 | CHEMBL2384165 | | ChEMBL | DHFR | 9 | 0.89 | 0.87 | 0.72 | CHEMBL4734506 | | ChEMBL | DHODH | 10 | 1.10 | 0.70 | 0.73 | CHEMBL2388704 | | ChEMBL | DHODH | 27 | 1.71 | 0.18 | 0.33 | CHEMBL4618428 | | ChEMBL | DHODH | 14 | 1.42 | 0.41 | 0.38 | CHEMBL4703073 | | ChEMBL | DHODH | 9 | 0.77 | 0.90 | 0.78 | CHEMBL863437 | | ChEMBL | DHODH | 15 | 1.39 | 0.85 | 0.78 | CHEMBL879486 | | ChEMBL | DOT1L | 8 | 2.29 | 0.90 | 0.79 | CHEMBL4480297 | | ChEMBL | DPP4 | 26 | 1.20 | 0.31 | 0.38 | CHEMBL1034787 | | ChEMBL | DPP4 | 23 | 0.78 | 0.33 | 0.43 | CHEMBL1058857 | | ChEMBL | DPP4 | 20 | 1.10 | 0.32 | 0.42 | CHEMBL2162559 | | ChEMBL | DPP4 | 18 | 0.72 | 0.27 | 0.44 | CHEMBL2444439 | | ChEMBL | DPP4 | 15 | 1.60 | 0.39 | 0.48 | CHEMBL3620564 | | ChEMBL | DPP4 | 23 | 0.74 | 0.61 | 0.50 | CHEMBL951312 | | ChEMBL | DUT | 18 | 0.83 | 0.51 | 0.45 | CHEMBL2049243 | | ChEMBL | DUT | 13 | 1.10 | 0.40 | 0.49 | CHEMBL2060493 | | ChEMBL | DYRK1A | 31 | 1.25 | 0.37 | 0.44 | CHEMBL3097668 | | ChEMBL | DYRK1A | 18 | 1.77 | 0.69 | 0.63 | CHEMBL5034566 | | ChEMBL | DYRK1B | 12 | 0.92 | 0.37 | 0.49 | CHEMBL3424978 | | ChEMBL | DYRK2 | 19 | 0.81 | 0.22 | 0.30 | CHEMBL5042808 | | ChEMBL | EED | 30 | 1.23 | 0.28 | 0.41 | CHEMBL4007108 | | ChEMBL | EED | 13 | 1.20 | 0.26 | 0.36 | CHEMBL4020039 | | ChEMBL | EED | 14 | 1.65 | 0.21 | 0.38 | CHEMBL4020042 | | ChEMBL | EGFR | 24 | 1.41 | 0.18 | 0.24 | CHEMBL1920033 | | ChEMBL | EGFR | 14 | 0.80 | 0.29 | 0.41 | CHEMBL1935838 | | ChEMBL | EGFR | 15 | 0.98 | 0.26 | 0.39 | CHEMBL3372999 | | ChEMBL | EGFR | 11 | 1.03 | 0.36 | 0.53 | CHEMBL5260455 | | ChEMBL | EHMT2 | 18 | 1.12 | 0.19 | 0.28 | CHEMBL4728050 | | ChEMBL | EIF2AK3 | 12 | 1.17 | 0.65 | 0.60 | CHEMBL2444392 | | ChEMBL | EPHX2 | 23 | 1.94 | 0.34 | 0.53 | CHEMBL1058191 | | ChEMBL | EPHX2 | 35 | 1.33 | 0.52 | 0.57 | CHEMBL1074708 | | ChEMBL | EPHX2 | 27 | 1.08 | 0.59 | 0.66 | CHEMBL2393704 | | ChEMBL | EPHX2 | 31 | 0.76 | 0.49 | 0.41 | CHEMBL3361515 | | ChEMBL | ERN1 | 20 | 1.57 | 0.50 | 0.61 | CHEMBL4673066 | | ChEMBL | ESR1 | 13 | 1.30 | 0.22 | 0.30 | CHEMBL679321 | | ChEMBL | ESR1 | 19 | 0.82 | 0.31 | 0.55 | CHEMBL831077 | | ChEMBL | ESR1 | 18 | 1.08 | 0.19 | 0.28 | CHEMBL832786 | | ChEMBL | ESR1 | 9 | 0.99 | 0.41 | 0.50 | CHEMBL867062 | | ChEMBL | ESR1 | 16 | 1.17 | 0.44 | 0.62 | CHEMBL886514 | | ChEMBL | ESRRG | 20 | 1.12 | 0.19 | 0.32 | CHEMBL3857086 | | ChEMBL | ESRRG | 25 | 1.41 | 0.45 | 0.38 | CHEMBL4413805 | | ChEMBL | ESRRG | 9 | 0.95 | 0.41 | 0.48 | CHEMBL867061 | | ChEMBL | F10 | 20 | 1.08 | 0.27 | 0.24 | CHEMBL1111059 | | ChEMBL | F10 | 21 | 1.74 | 0.21 | 0.32 | CHEMBL1687149 | | ChEMBL | F10 | 34 | 1.54 | 0.75 | 0.60 | CHEMBL1925585 | | ChEMBL | F10 | 17 | 1.16 | 0.38 | 0.43 | CHEMBL3371468 | | ChEMBL | F10 | 27 | 1.07 | 0.37 | 0.41 | CHEMBL5107327 | | ChEMBL | F10 | 15 | 1.17 | 0.25 | 0.36 | CHEMBL657275 | | ChEMBL | F10 | 14 | 1.13 | 0.63 | 0.67 | CHEMBL661585 | | ChEMBL | F10 | 13 | 0.85 | 0.41 | 0.51 | CHEMBL661586 | | ChEMBL | F10 | 28 | 1.19 | 0.50 | 0.53 | CHEMBL661794 | | ChEMBL | F10 | 4 | 0.56 | 0.55 | 0.33 | CHEMBL661801 | | ChEMBL | F10 | 15 | 0.79 | 0.34 | 0.28 | CHEMBL662878 | | ChEMBL | F10 | 18 | 0.80 | 0.22 | 0.41 | CHEMBL827928 | | ChEMBL | F10 | 36 | 1.11 | 0.20 | 0.28 | CHEMBL889317 | | ChEMBL | F10 | 36 | 1.84 | 0.37 | 0.32 | CHEMBL900663 | | ChEMBL | F10 | 9 | 0.75 | 0.72 | 0.56 | CHEMBL906423 | | ChEMBL | F11 | 25 | 1.15 | 0.56 | 0.58 | CHEMBL3129742 | | ChEMBL | F2 | 16 | 0.84 | 0.65 | 0.58 | CHEMBL1067528 | | ChEMBL | F2 | 33 | 1.89 | 0.32 | 0.41 | CHEMBL3424914 | | ChEMBL | F2 | 14 | 0.78 | 0.82 | 0.71 | CHEMBL4479424 | | ChEMBL | F2 | 18 | 1.90 | 0.20 | 0.41 | CHEMBL808337 | | ChEMBL | F2 | 18 | 1.45 | 0.23 | 0.43 | CHEMBL813625 | | ChEMBL | F2 | 24 | 1.10 | 0.66 | 0.60 | CHEMBL870018 | | ChEMBL | F2 | 24 | 1.74 | 0.22 | 0.35 | CHEMBL884569 | | ChEMBL | F2 | 9 | 0.44 | 0.96 | 0.89 | CHEMBL924350 | | ChEMBL | F2 | 17 | 0.82 | 0.24 | 0.41 | CHEMBL934691 | | ChEMBL | F7 | 16 | 1.35 | 0.62 | 0.64 | CHEMBL1005612 | | ChEMBL | F7 | 22 | 1.51 | 0.38 | 0.39 | CHEMBL3129741 | | ChEMBL | FABP4 | 35 | 0.86 | 0.39 | 0.53 | CHEMBL3888563 | | ChEMBL | FKBP1A | 10 | 0.70 | 0.66 | 0.42 | CHEMBL678145 | | ChEMBL | GAK | 21 | 1.11 | 0.63 | 0.56 | CHEMBL4736826 | | ChEMBL | GAK | 9 | 0.96 | 0.33 | 0.44 | CHEMBL5217398 | | ChEMBL | GCKR | 24 | 1.14 | 0.72 | 0.70 | CHEMBL3131528 | | ChEMBL | GCKR | 11 | 0.69 | 0.87 | 0.67 | CHEMBL3751185 | | ChEMBL | GCKR | 11 | 0.74 | 0.87 | 0.67 | CHEMBL3751192 | | ChEMBL | GRK2 | 14 | 1.14 | 0.46 | 0.47 | CHEMBL4703614 | | ChEMBL | GSK3B | 25 | 0.75 | 0.73 | 0.71 | CHEMBL1031513 | | ChEMBL | GSK3B | 22 | 1.31 | 0.58 | 0.53 | CHEMBL1102983 | | ChEMBL | GSK3B | 20 | 1.10 | 0.43 | 0.56 | CHEMBL1960393 | | ChEMBL | GSK3B | 34 | 1.33 | 0.46 | 0.40 | CHEMBL5252935 | | ChEMBL | HSP90AA1 | 18 | 0.98 | 0.29 | 0.11 | CHEMBL3107812 | | ChEMBL | HSP90AA1 | 9 | 0.99 | 0.62 | 0.67 | CHEMBL3427922 | | ChEMBL | HSP90AA1 | 23 | 1.60 | 0.38 | 0.44 | CHEMBL3885742 | | ChEMBL | HSP90AA1 | 7 | 0.74 | 0.34 | 0.59 | CHEMBL4372487 | | ChEMBL | HSP90AA1 | 11 | 0.67 | 0.76 | 0.56 | CHEMBL832973 | | ChEMBL | IDH2 | 14 | 1.16 | 0.32 | 0.45 | CHEMBL4628662 | | ChEMBL | IGF1R | 9 | 1.08 | 0.38 | 0.54 | CHEMBL1045057 | | ChEMBL | IGF1R | 11 | 1.03 | 0.49 | 0.53 | CHEMBL3424980 | | ChEMBL | IRAK4 | 19 | 0.84 | 0.50 | 0.58 | CHEMBL4015947 | | ChEMBL | IRAK4 | 37 | 1.17 | 0.57 | 0.50 | CHEMBL4047622 | | ChEMBL | IRAK4 | 14 | 1.26 | 0.48 | 0.53 | CHEMBL4323523 | | ChEMBL | JAK1 | 21 | 0.91 | 0.31 | 0.36 | CHEMBL2160360 | | ChEMBL | JAK1 | 21 | 1.55 | 0.29 | 0.38 | CHEMBL2395113 | | ChEMBL | JAK1 | 31 | 0.63 | 0.72 | 0.66 | CHEMBL2438692 | | ChEMBL | JAK1 | 23 | 0.95 | 0.63 | 0.57 | CHEMBL3706193 | | ChEMBL | JAK1 | 23 | 0.91 | 0.52 | 0.54 | CHEMBL3784138 | | ChEMBL | JAK1 | 14 | 1.37 | 0.32 | 0.23 | CHEMBL4411594 | | ChEMBL | JAK1 | 38 | 1.75 | 0.22 | 0.39 | CHEMBL4612619 | | ChEMBL | JAK1 | 10 | 0.51 | 0.65 | 0.72 | CHEMBL4620434 | | ChEMBL | JAK2 | 37 | 1.04 | 0.47 | 0.50 | CHEMBL1044318 | | ChEMBL | JAK2 | 20 | 1.24 | 0.37 | 0.54 | CHEMBL1116984 | | ChEMBL | JAK2 | 29 | 0.77 | 0.77 | 0.58 | CHEMBL1685409 | | ChEMBL | JAK2 | 13 | 0.69 | 0.47 | 0.40 | CHEMBL2160361 | | ChEMBL | JAK2 | 34 | 1.00 | 0.57 | 0.61 | CHEMBL2421805 | | ChEMBL | JAK2 | 30 | 0.86 | 0.42 | 0.42 | CHEMBL3374493 | | ChEMBL | JAK2 | 16 | 1.41 | 0.64 | 0.62 | CHEMBL3404501 | | ChEMBL | JAK2 | 15 | 0.84 | 0.42 | 0.45 | CHEMBL3625473 | | ChEMBL | JAK2 | 10 | 1.39 | 0.42 | 0.54 | CHEMBL3625512 | | ChEMBL | JAK2 | 12 | 0.69 | 0.60 | 0.42 | CHEMBL3627422 | | ChEMBL | JAK2 | 9 | 1.30 | 0.77 | 0.56 | CHEMBL4031305 | | ChEMBL | JAK2 | 8 | 1.36 | 0.23 | 0.07 | CHEMBL4046590 | | ChEMBL | JAK2 | 15 | 0.83 | 0.55 | 0.44 | CHEMBL4150584 | | ChEMBL | KDR | 25 | 1.39 | 0.50 | 0.44 | CHEMBL2027406 | | ChEMBL | KIF11 | 16 | 0.81 | 0.40 | 0.38 | CHEMBL1023928 | | ChEMBL | KIF11 | 14 | 0.70 | 0.61 | 0.59 | CHEMBL1037992 | | ChEMBL | KIF11 | 22 | 1.10 | 0.58 | 0.62 | CHEMBL1694081 | | ChEMBL | KIF11 | 17 | 1.30 | 0.33 | 0.23 | CHEMBL3636399 | | ChEMBL | KIF11 | 22 | 1.30 | 0.37 | 0.43 | CHEMBL831535 | | ChEMBL | KIF11 | 10 | 1.49 | 0.33 | 0.42 | CHEMBL942113 | | ChEMBL | KLK3 | 26 | 1.01 | 0.61 | 0.64 | CHEMBL4844448 | | ChEMBL | KLK7 | 17 | 0.74 | 0.18 | 0.39 | CHEMBL4125121 | | ChEMBL | LCK | 19 | 0.93 | 0.36 | 0.34 | CHEMBL902547 | | ChEMBL | LCK | 11 | 0.59 | 0.74 | 0.64 | CHEMBL903614 | | ChEMBL | LCK | 32 | 1.98 | 0.31 | 0.40 | CHEMBL913225 | | ChEMBL | LCK | 12 | 1.49 | 0.49 | 0.39 | CHEMBL948988 | | ChEMBL | LCK | 25 | 1.99 | 0.41 | 0.52 | CHEMBL951931 | | ChEMBL | LDHA | 12 | 1.79 | 0.27 | 0.42 | CHEMBL3369987 | | ChEMBL | LDHA | 13 | 0.84 | 0.65 | 0.49 | CHEMBL5138278 | | ChEMBL | MAOB | 7 | 1.67 | 0.61 | 0.43 | CHEMBL3588480 | | ChEMBL | MAP2K1 | 18 | 1.32 | 0.57 | 0.08 | CHEMBL1686836 | | ChEMBL | MAP2K1 | 10 | 0.86 | 0.28 | 0.18 | CHEMBL2092007 | | ChEMBL | MAP2K1 | 22 | 1.00 | 0.47 | 0.45 | CHEMBL3096357 | | ChEMBL | MAP2K1 | 22 | 1.17 | 0.24 | 0.40 | CHEMBL3266112 | | ChEMBL | MAP3K5 | 17 | 1.00 | 0.56 | 0.26 | CHEMBL4605628 | | ChEMBL | MAP4K4 | 19 | 0.85 | 0.39 | 0.49 | CHEMBL3265752 | | ChEMBL | MAP4K4 | 12 | 0.77 | 0.41 | 0.26 | CHEMBL3624922 | | ChEMBL | MAP4K4 | 15 | 0.53 | 0.75 | 0.62 | CHEMBL3755426 | | ChEMBL | MAPK10 | 32 | 1.00 | 0.22 | 0.31 | CHEMBL1063579 | | ChEMBL | MAPK10 | 26 | 1.12 | 0.43 | 0.37 | CHEMBL2379720 | | ChEMBL | MAPK10 | 17 | 1.49 | 0.40 | 0.43 | CHEMBL3375438 | | ChEMBL | MAPK10 | 18 | 0.73 | 0.45 | 0.41 | CHEMBL3578950 | | ChEMBL | MAPK14 | 11 | 0.66 | 0.52 | 0.50 | CHEMBL1024853 | | ChEMBL | MAPK14 | 24 | 0.84 | 0.58 | 0.60 | CHEMBL1053415 | | ChEMBL | MAPK14 | 8 | 0.65 | 0.66 | 0.50 | CHEMBL1101788 | | ChEMBL | MAPK14 | 19 | 1.18 | 0.31 | 0.31 | CHEMBL1110043 | | ChEMBL | MAPK14 | 21 | 0.83 | 0.52 | 0.49 | CHEMBL1251166 | | ChEMBL | MAPK14 | 35 | 0.88 | 0.41 | 0.47 | CHEMBL1769102 | | ChEMBL | MAPK14 | 18 | 1.30 | 0.70 | 0.37 | CHEMBL1787752 | | ChEMBL | MAPK14 | 17 | 1.36 | 0.26 | 0.40 | CHEMBL1804666 | | ChEMBL | MAPK14 | 8 | 0.73 | 0.40 | 0.50 | CHEMBL1805307 | | ChEMBL | MAPK14 | 17 | 1.05 | 0.67 | 0.70 | CHEMBL1825474 | | ChEMBL | MAPK14 | 19 | 1.07 | 0.48 | 0.57 | CHEMBL1825475 | | ChEMBL | MAPK14 | 21 | 1.80 | 0.29 | 0.31 | CHEMBL1913342 | | ChEMBL | MAPK14 | 11 | 1.47 | 0.45 | 0.70 | CHEMBL2061259 | | ChEMBL | MAPK14 | 29 | 0.90 | 0.31 | 0.44 | CHEMBL2317232 | | ChEMBL | MAPK14 | 35 | 1.57 | 0.33 | 0.33 | CHEMBL3705800 | | ChEMBL | MAPK14 | 17 | 1.79 | 0.39 | 0.53 | CHEMBL732094 | | ChEMBL | MAPK14 | 9 | 1.42 | 0.68 | 0.56 | CHEMBL734085 | | ChEMBL | MAPK14 | 9 | 1.65 | 0.54 | 0.56 | CHEMBL734088 | | ChEMBL | MAPK14 | 35 | 1.17 | 0.28 | 0.31 | CHEMBL859283 | | ChEMBL | MAPK14 | 17 | 1.03 | 0.58 | 0.66 | CHEMBL929947 | | ChEMBL | MAPK14 | 5 | 0.96 | 0.57 | 0.40 | CHEMBL983811 | | ChEMBL | MAPK14 | 13 | 1.93 | 0.33 | 0.41 | CHEMBL997720 | | ChEMBL | MAPK1 | 21 | 1.03 | 0.38 | 0.45 | CHEMBL4425912 | | ChEMBL | MAPK7 | 26 | 0.99 | 0.38 | 0.37 | CHEMBL5166085 | | ChEMBL | MAPK8 | 29 | 0.95 | 0.37 | 0.43 | CHEMBL2429340 | | ChEMBL | MAPKAPK2 | 17 | 1.33 | 0.19 | 0.40 | CHEMBL1072653 | | ChEMBL | MCL1 | 20 | 1.45 | 0.80 | 0.61 | CHEMBL3429294 | | ChEMBL | MDM2 | 12 | 0.46 | 0.31 | 0.30 | CHEMBL3705138 | | ChEMBL | MELK | 13 | 0.91 | 0.57 | 0.35 | CHEMBL3824963 | | ChEMBL | MELK | 8 | 0.79 | 0.72 | 0.62 | CHEMBL4006633 | | ChEMBL | METAP2 | 34 | 1.48 | 0.31 | 0.24 | CHEMBL4397057 | | ChEMBL | MET | 10 | 0.78 | 0.34 | 0.40 | CHEMBL1038130 | | ChEMBL | MET | 8 | 1.05 | 0.90 | 0.79 | CHEMBL2032485 | | ChEMBL | MET | 22 | 2.00 | 0.71 | 0.51 | CHEMBL3226601 | | ChEMBL | MET | 21 | 0.94 | 0.61 | 0.59 | CHEMBL3404455 | | ChEMBL | MET | 27 | 1.30 | 0.58 | 0.41 | CHEMBL3418289 | | ChEMBL | MET | 9 | 1.08 | 0.51 | 0.11 | CHEMBL3816036 | | ChEMBL | MET | 16 | 0.60 | 0.61 | 0.66 | CHEMBL4426787 | | ChEMBL | MMP13 | 13 | 1.22 | 0.83 | 0.58 | CHEMBL1798873 | | ChEMBL | MMP13 | 31 | 1.25 | 0.69 | 0.57 | CHEMBL3373425 | | ChEMBL | MMP13 | 34 | 1.03 | 0.59 | 0.57 | CHEMBL3388707 | | ChEMBL | MTAP | 17 | 0.98 | 0.40 | 0.38 | CHEMBL2073357 | | ChEMBL | NAMPT | 36 | 1.21 | 0.30 | 0.31 | CHEMBL2396492 | | ChEMBL | NAMPT | 38 | 1.01 | 0.42 | 0.53 | CHEMBL4036655 | | ChEMBL | NEK2 | 11 | 1.12 | 0.35 | 0.45 | CHEMBL1693342 | | ChEMBL | NEK2 | 19 | 1.42 | 0.42 | 0.46 | CHEMBL2044151 | | ChEMBL | NR1H2 | 8 | 1.61 | 0.63 | 0.64 | CHEMBL907758 | | ChEMBL | NR3C1 | 21 | 1.19 | 0.67 | 0.62 | CHEMBL4031186 | | ChEMBL | NTRK1 | 10 | 1.13 | 0.39 | 0.38 | CHEMBL5146064 | | ChEMBL | NUDT1 | 9 | 1.75 | 0.31 | 0.48 | CHEMBL4673830 | | ChEMBL | OGA | 10 | 0.96 | 0.52 | 0.42 | CHEMBL3887929 | | ChEMBL | OGA | 31 | 1.95 | 0.20 | 0.33 | CHEMBL4355754 | | ChEMBL | PAK4 | 38 | 1.97 | 0.66 | 0.66 | CHEMBL4033368 | | ChEMBL | PARP1 | 36 | 1.46 | 0.20 | 0.49 | CHEMBL1010815 | | ChEMBL | PARP1 | 28 | 1.68 | 0.61 | 0.54 | CHEMBL1115415 | | ChEMBL | PARP2 | 16 | 1.45 | 0.35 | 0.55 | CHEMBL3607347 | | ChEMBL | PDE10A | 36 | 0.73 | 0.44 | 0.48 | CHEMBL1780568 | | ChEMBL | PDE10A | 28 | 1.06 | 0.47 | 0.56 | CHEMBL1960211 | | ChEMBL | PDE10A | 33 | 0.86 | 0.27 | 0.31 | CHEMBL2020845 | | ChEMBL | PDE10A | 33 | 0.77 | 0.23 | 0.30 | CHEMBL2071880 | | ChEMBL | PDE10A | 17 | 1.46 | 0.37 | 0.50 | CHEMBL3297609 | | ChEMBL | PDE10A | 28 | 1.59 | 0.55 | 0.61 | CHEMBL3632375 | | ChEMBL | PDE1B | 13 | 1.16 | 0.51 | 0.53 | CHEMBL4011522 | | ChEMBL | PDE2A | 21 | 1.30 | 0.50 | 0.56 | CHEMBL4008514 | | ChEMBL | PDE4B | 13 | 0.62 | 0.79 | 0.68 | CHEMBL3374901 | | ChEMBL | PDE4D | 12 | 1.05 | 0.55 | 0.61 | CHEMBL3374902 | | ChEMBL | PDE4D | 21 | 1.18 | 0.39 | 0.43 | CHEMBL3375590 | | ChEMBL | PDE5A | 12 | 1.58 | 0.24 | 0.38 | CHEMBL1107382 | | ChEMBL | PDE5A | 22 | 1.74 | 0.50 | 0.43 | CHEMBL2184512 | | ChEMBL | PDE5A | 14 | 0.80 | 0.48 | 0.54 | CHEMBL968866 | | ChEMBL | PDK2 | 20 | 0.45 | 0.88 | 0.82 | CHEMBL5057865 | | ChEMBL | PDPK1 | 11 | 1.01 | 0.53 | 0.20 | CHEMBL1942054 | | ChEMBL | PDPK1 | 22 | 1.36 | 0.37 | 0.55 | CHEMBL3815750 | | ChEMBL | PFKFB3 | 26 | 1.50 | 0.41 | 0.55 | CHEMBL3425140 | | ChEMBL | PGR | 15 | 1.67 | 0.35 | 0.39 | CHEMBL1054361 | | ChEMBL | PHGDH | 16 | 0.86 | 0.67 | 0.57 | CHEMBL4375168 | | ChEMBL | PIK3C3 | 17 | 0.84 | 0.23 | 0.32 | CHEMBL3784185 | | ChEMBL | PIK3CA | 27 | 1.80 | 0.31 | 0.41 | CHEMBL3116932 | | ChEMBL | PIK3CA | 27 | 1.64 | 0.26 | 0.17 | CHEMBL3611486 | | ChEMBL | PIK3CA | 21 | 1.72 | 0.41 | 0.50 | CHEMBL4360966 | | ChEMBL | PIK3CA | 31 | 0.87 | 0.58 | 0.55 | CHEMBL5153851 | | ChEMBL | PIK3CA | 15 | 1.61 | 0.22 | 0.26 | CHEMBL887586 | | ChEMBL | PIK3CG | 22 | 0.97 | 0.24 | 0.42 | CHEMBL1065056 | | ChEMBL | PIK3CG | 9 | 0.63 | 0.79 | 0.67 | CHEMBL1108628 | | ChEMBL | PIK3CG | 10 | 1.04 | 0.50 | 0.47 | CHEMBL2174949 | | ChEMBL | PIM1 | 16 | 0.95 | 0.47 | 0.48 | CHEMBL1022925 | | ChEMBL | PIM1 | 12 | 0.77 | 0.55 | 0.50 | CHEMBL2038828 | | ChEMBL | PIM1 | 14 | 1.72 | 0.36 | 0.42 | CHEMBL2149642 | | ChEMBL | PIM1 | 17 | 1.99 | 0.60 | 0.50 | CHEMBL3106177 | | ChEMBL | PIM1 | 35 | 1.21 | 0.52 | 0.57 | CHEMBL3301295 | | ChEMBL | PIM1 | 13 | 1.28 | 0.69 | 0.71 | CHEMBL3376646 | | ChEMBL | PIM1 | 17 | 1.37 | 0.48 | 0.41 | CHEMBL3887608 | | ChEMBL | PIM1 | 15 | 1.31 | 0.21 | 0.45 | CHEMBL4222672 | | ChEMBL | PIM2 | 12 | 0.93 | 0.74 | 0.61 | CHEMBL3376647 | | ChEMBL | PLA2G7 | 19 | 0.95 | 0.47 | 0.49 | CHEMBL3861790 | | ChEMBL | PLA2G7 | 23 | 1.09 | 0.40 | 0.53 | CHEMBL707410 | | ChEMBL | PLAU | 21 | 1.19 | 0.61 | 0.64 | CHEMBL1026932 | | ChEMBL | PLG | 10 | 1.44 | 0.70 | 0.47 | CHEMBL3295545 | | ChEMBL | PNMT | 9 | 0.52 | 0.89 | 0.94 | CHEMBL890212 | | ChEMBL | PNP | 3 | 1.33 | 0.25 | 0.33 | CHEMBL951777 | | ChEMBL | PPARD | 11 | 1.25 | 0.67 | 0.60 | CHEMBL759401 | | ChEMBL | PPARG | 28 | 1.29 | 0.70 | 0.63 | CHEMBL1004952 | | ChEMBL | PPARG | 26 | 1.30 | 0.31 | 0.43 | CHEMBL1947820 | | ChEMBL | PPARG | 22 | 1.88 | 0.34 | 0.44 | CHEMBL827222 | | ChEMBL | PPARG | 9 | 1.15 | 0.23 | 0.42 | CHEMBL830853 | | ChEMBL | PPARG | 12 | 1.23 | 0.36 | 0.52 | CHEMBL980390 | | ChEMBL | PTGES | 11 | 1.09 | 0.69 | 0.61 | CHEMBL3999537 | | ChEMBL | PTK2B | 19 | 0.73 | 0.45 | 0.39 | CHEMBL960612 | | ChEMBL | PTK2 | 23 | 1.03 | 0.41 | 0.44 | CHEMBL4832051 | | ChEMBL | PTK2 | 23 | 1.26 | 0.86 | 0.73 | CHEMBL962347 | | ChEMBL | RAF1 | 11 | 1.47 | 0.53 | 0.44 | CHEMBL3267830 | | ChEMBL | RARG | 17 | 1.35 | 0.39 | 0.40 | CHEMBL798022 | | ChEMBL | RBP4 | 21 | 1.28 | 0.38 | 0.41 | CHEMBL3380009 | | ChEMBL | RBP4 | 31 | 1.59 | 0.36 | 0.45 | CHEMBL3594968 | | ChEMBL | REN | 29 | 1.40 | 0.67 | 0.61 | CHEMBL1039372 | | ChEMBL | REN | 26 | 1.52 | 0.58 | 0.56 | CHEMBL1039373 | | ChEMBL | REN | 16 | 1.60 | 0.42 | 0.41 | CHEMBL1054383 | | ChEMBL | REN | 23 | 1.18 | 0.62 | 0.43 | CHEMBL3406487 | | ChEMBL | REN | 12 | 1.22 | 0.28 | 0.42 | CHEMBL828516 | | ChEMBL | REN | 15 | 0.78 | 0.59 | 0.58 | CHEMBL898576 | | ChEMBL | REN | 33 | 1.18 | 0.30 | 0.41 | CHEMBL957839 | | ChEMBL | RET | 10 | 1.21 | 0.60 | 0.56 | CHEMBL4836452 | | ChEMBL | RIPK2 | 33 | 1.37 | 0.47 | 0.47 | CHEMBL4135584 | | ChEMBL | RIPK2 | 12 | 1.20 | 0.46 | 0.52 | CHEMBL4269599 | | ChEMBL | RIPK2 | 28 | 1.77 | 0.22 | 0.44 | CHEMBL4771083 | | ChEMBL | ROCK2 | 26 | 0.79 | 0.21 | 0.30 | CHEMBL2444040 | | ChEMBL | ROCK2 | 12 | 1.14 | 0.38 | 0.39 | CHEMBL4669834 | | ChEMBL | RORC | 22 | 1.38 | 0.21 | 0.31 | CHEMBL3270932 | | ChEMBL | RORC | 36 | 1.12 | 0.48 | 0.36 | CHEMBL3599133 | | ChEMBL | RORC | 22 | 1.23 | 0.33 | 0.32 | CHEMBL4197717 | | ChEMBL | RPS6KA3 | 28 | 0.79 | 0.58 | 0.62 | CHEMBL3607765 | | ChEMBL | RPS6KA3 | 12 | 0.89 | 0.83 | 0.72 | CHEMBL4266990 | | ChEMBL | RPS6KA3 | 9 | 1.13 | 0.59 | 0.56 | CHEMBL4266991 | | ChEMBL | RXRA | 10 | 0.99 | 0.64 | 0.64 | CHEMBL797916 | | ChEMBL | SLC5A2 | 10 | 1.07 | 0.56 | 0.69 | CHEMBL1217373 | | ChEMBL | SLC6A1 | 15 | 0.97 | 0.40 | 0.37 | CHEMBL862288 | | ChEMBL | SLC6A2 | 18 | 0.74 | 0.42 | 0.42 | CHEMBL2211273 | | ChEMBL | SMYD2 | 9 | 1.29 | 0.59 | 0.50 | CHEMBL3592282 | | ChEMBL | SPR | 12 | 0.88 | 0.47 | 0.53 | CHEMBL3887419 | | ChEMBL | SPR | 11 | 0.88 | 0.43 | 0.38 | CHEMBL3887420 | | ChEMBL | SRC | 10 | 1.36 | 0.90 | 0.73 | CHEMBL2039537 | | ChEMBL | SRC | 17 | 0.88 | 0.50 | 0.46 | CHEMBL823232 | | ChEMBL | STK3 | 8 | 0.71 | 0.42 | 0.64 | CHEMBL3395732 | | ChEMBL | SYK | 21 | 1.56 | 0.29 | 0.31 | CHEMBL1838853 | | ChEMBL | SYK | 21 | 0.76 | 0.28 | 0.11 | CHEMBL945309 | | ChEMBL | TEK | 24 | 1.98 | 0.24 | 0.36 | CHEMBL908503 | | ChEMBL | TNKS | 9 | 0.72 | 0.84 | 0.87 | CHEMBL2384487 | | ChEMBL | TPH1 | 38 | 1.03 | 0.20 | 0.12 | CHEMBL4001798 | | ChEMBL | TRAP1 | 8 | 1.33 | 0.57 | 0.21 | CHEMBL3427925 | | ChEMBL | TTBK1 | 20 | 1.71 | 0.26 | 0.25 | CHEMBL5236876 | | ChEMBL | TTK | 13 | 1.24 | 0.31 | 0.46 | CHEMBL2383388 | | ChEMBL | TTK | 25 | 0.86 | 0.74 | 0.73 | CHEMBL3411333 | | ChEMBL | TYMS | 17 | 0.95 | 0.31 | 0.33 | CHEMBL823516 | | ChEMBL | USP7 | 12 | 1.22 | 0.28 | 0.00 | CHEMBL5234060 | | ChEMBL | WDR5 | 38 | 1.78 | 0.47 | 0.56 | CHEMBL3875502 | | ChEMBL | WEE1 | 10 | 1.44 | 0.48 | 0.58 | CHEMBL5230681 | | CyclicPeptide | Menin | 16 | 0.90 | 0.46 | 0.50 | | | CyclicPeptide | PCSK9 | 18 | 0.77 | 0.51 | 0.47 | | | GPCR | A2A | 10 | 0.76 | 0.83 | 0.69 | Deflorian | | GPCR | A2A | 7 | 0.54 | 0.84 | 0.62 | Lenselink | | GPCR | A2A | 9 | 0.91 | 0.50 | 0.39 | Minetti | | GPCR | A2A | 7 | 0.38 | 0.33 | 0.62 | Piersanti | | GPCR | CXCR4 | 9 | 1.11 | 0.44 | 0.25 | | | GPCR | D3 | 6 | 1.09 | 0.67 | 0.87 | | | GPCR | DOR | 11 | 0.83 | 0.59 | 0.60 | | | GPCR | OX2-set1 | 27 | 0.88 | 0.57 | 0.57 | | | GPCR | OX2-set2 | 24 | 1.07 | 0.25 | 0.35 | | | GPCR | TA1 | 8 | 1.07 | 0.58 | 0.43 | | | GPCR | beta1 | 9 | 0.91 | 0.14 | 0.22 | | | GPCR | mGluR5 | 12 | 1.16 | 0.73 | 0.79 | | | Hermite | 3CLPro | 5 | 0.83 | 0.69 | 0.80 | | | Hermite | ACK1 | 6 | 1.10 | 0.71 | 0.60 | | | Hermite | BCL6 | 6 | 1.01 | 0.84 | 0.60 | | | Hermite | CDK4 | 6 | 0.38 | 0.84 | 0.87 | | | Hermite | Eg5 | 7 | 0.40 | 0.58 | 0.52 | | | Hermite | FKBP12 | 6 | 0.53 | 0.84 | 0.87 | | | Hermite | FXR | 6 | 0.69 | 0.69 | 0.60 | | | Hermite | Galectin-3 | 8 | 0.90 | 0.89 | 0.93 | | | Hermite | HNE | 6 | 1.28 | 0.96 | 0.73 | | | Hermite | HSP90 | 11 | 1.29 | 0.71 | 0.73 | | | Hermite | KRAS-G12D | 10 | 0.76 | 0.91 | 0.87 | | | Hermite | PAK4 | 10 | 0.58 | 0.66 | 0.64 | | | Hermite | Pka | 8 | 0.51 | 0.87 | 0.79 | | | Hermite | mGluR5 | 12 | 1.16 | 0.73 | 0.78 | | | JACS8 | BACE | 36 | 0.80 | 0.47 | 0.49 | | | JACS8 | CDK2 | 16 | 0.81 | 0.54 | 0.53 | | | JACS8 | JNK1 | 21 | 0.65 | 0.59 | 0.63 | | | JACS8 | MCL1 | 42 | 1.19 | 0.57 | 0.57 | | | JACS8 | P38 | 34 | 0.92 | 0.42 | 0.54 | | | JACS8 | PTP1B | 23 | 0.91 | 0.57 | 0.67 | | | JACS8 | TYK2 | 16 | 0.81 | 0.63 | 0.55 | | | JACS8 | Thrombin | 11 | 0.78 | 0.66 | 0.64 | | | Merck8 | CDK8 | 32 | 0.87 | 0.84 | 0.70 | | | Merck8 | EG5 | 28 | 0.84 | 0.54 | 0.46 | | | Merck8 | HIF-2 | 41 | 1.54 | 0.22 | 0.28 | | | Merck8 | PFKFB3 | 40 | 1.06 | 0.39 | 0.44 | | | Merck8 | SHP2 | 26 | 1.79 | 0.04 | 0.12 | | | Merck8 | SYK | 48 | 1.56 | 0.26 | 0.42 | | | Merck8 | TNKS2 | 33 | 1.03 | 0.24 | 0.28 | | | Merck8 | c-Met | 24 | 1.01 | 0.79 | 0.73 | | | WaterSet | Brd4(1)-ASH106 | 8 | 0.66 | 0.62 | 0.79 | | | WaterSet | Chk1 | 13 | 1.02 | 0.53 | 0.61 | | | WaterSet | HSP90 | 11 | 1.20 | 0.65 | 0.56 | Kung | | WaterSet | HSP90 | 4 | 0.43 | 0.95 | 1.00 | Woodhead | | WaterSet | Scytalone-Dehydratase | 7 | 1.35 | 0.71 | 0.62 | | | WaterSet | Taf1(2) | 8 | 0.46 | 0.67 | 0.36 | | | WaterSet | Thrombin | 21 | 0.79 | 0.56 | 0.58 | | | WaterSet | Urokinase | 4 | 0.55 | 0.60 | 1.00 | |

Repository Structure

Each system is organized into a separate folder, containing:

``` scripts/ genfigure.py # Script for generating dG comparison plots based on resultdG.csv

unifepbenchmarks/ system1/
README.md # Brief description of the system
protein.pdb # Protein structure file in PDB format
refligand.sdf # Reference ligand file in SDF format
resultdG.png # Visualization of FEP-calculated dG
resultdG.csv # Numerical results of dG comparisons

system2/
README.md
protein.pdb
refligand.sdf
resultdG.png
resultdG.csv

... ```

File Descriptions

• README.md: Contains a brief summary of the system, including error statistics (e.g., RMSE of dG and ddG).
• protein.pdb: The protein structure file in PDB format required for FEP calculations.
• ref_ligand.sdf: The reference ligand file in SDF format used to define the ligand in the system.
• result_dG.png: Graphical representation of FEP-derived binding free energies (dG) compared to experimental values.
• result_dG.csv: A table containing RBFE-predicted binding free energies (fep_dG) and experimental measurements (exp_dG).

result_dG.csv Example (RBFE-calculated dG values)

| ligandsmiles | ligandname | expdG (kcal/mol) | fepdG (kcal/mol) | fepdGstd (kcal/mol) | |----------------|--------------|-----------------|-----------------|-----------------| | 'LigandSMILES' | 'LigandName' | -7.5 | -7.2 | 0.15 | | 'LigandSMILES' | 'LigandName' | -8.1 | -7.9 | 0.08 |

Data Update Guidelines

When submitting new benchmark data via a Merge Request, please provide the following:

1. Name all new folders using the format Series|Target|Description.
2. Include the required files in each system folder: protein.pdb and ref_ligand.sdf along with the existing files.
3. Update the benchmark summary table by running: cmd python scripts/update_summary_table.py

Citation

If you use Uni-FEP-Benchmarks in your research, please cite:

Zou, R., Wang, L., Wang, X., Ding, Y. and Zheng, H., 2025. Breaking Barriers in FEP Benchmarking: A Large-Scale Dataset Reflecting Real-World Drug Discovery Challenges. ChemRxiv. https://chemrxiv.org/engage/chemrxiv/article-details/687294afe1957b8c618d81e6