This repository contains data and findings from the study titled "Wide Transition-State Ensemble as Key Component for Enzyme Catalysis". It includes the following compressed files:

1. MSMD_simulations: Contains the MSMD simulation data, including topology, work vs. reaction coordinate, trajectories, and inputs. Both forward and backward reactions are included. Data for all systems are located in this folder: ADP/ADP with Mg²⁺, ADP/ADPH without Mg²⁺, and ADP/ADPH with Mg²⁺.

2. DFT_calculations: Contains data for the free energy profile of the reaction for the system ADP/ADP with Mg²⁺, using DFT level calculations for the QM region. This folder includes topology, work vs. reaction coordinate, trajectories, and inputs. Both forward and backward reactions are included.

3. Umbrella_Sampling: Contains data for: ADP/ADP with Mg²⁺ and ADP/ADPH without Mg²⁺. Includes topology, free energy profiles built using the WHAM method, trajectories, and reaction coordinate values for each umbrella sampling (US) simulation window.

4. Commitment_Analysis_[part1, part2, and part3]: Contains data for all systems in this folder: ADP/ADP with Mg²⁺ and ADP/ADPH without Mg²⁺. Includes simulation data (topology, inputs, outputs, trajectories) used for the committor plot and commitment analysis. Structures from MSMD forward and backward reactions were used as starting points. Ten replicas were performed for the analysis. The Python scripts for the committor plot and commitment analysis are commitment_plot.py and commitment_analysis.py, respectively.

5. Comparison_structures: Contains transition-state (TS) structures obtained from MSMD and Umbrella Sampling simulations. Also, it contains a script written in R that calculates the PCA analysis for both sets of TS structures.

The following files in Amber format are provided for each simulation:

• .prmtop: Contains the topological information of the solvated system (e.g., connectivity).
• .nc/.netcdf: Contains the raw trajectory of the simulation (without centering or imaging molecules).
• .rst7: Provides the initial coordinates.
• .RST: Amber restraint file specifying the reaction coordinate and other applied restraints.
• .mdin: Input control data for the simulation (e.g., number of steps, step time, temperature control).
• .dat: Contains the SMD output information along the reaction coordinate (e.g., work, force, reaction coordinate measured on the system).

Further details can be found in the README files within each directory. Below is the abstract of the corresponding study:

"Transition-state theory has provided the theoretical framework to explain the enormous rate accelerations of chemical reactions by enzymes. Given that proteins display large ensembles of conformations, unique transition states would pose a huge entropic bottleneck for enzyme catalysis. To shed light on this question, we studied the nature of the enzymatic transition state for the phosphoryl-transfer step in adenylate kinase by quantum-mechanics/molecular-mechanics calculations. We find a structurally wide set of energetically equivalent configurations that lie along the reaction coordinate and hence a broad transition-state ensemble (TSE). A conformationally delocalized ensemble, including asymmetric transition states, is rooted in the macroscopic nature of the enzyme. The computational results are buttressed by enzyme kinetics experiments that confirm the decrease of the entropy of activation predicted from such wide TSE. Transition-state ensembles as a key for efficient enzyme catalysis further boosts a unifying concept for protein folding and conformational transitions underlying protein function."

What is IPGOD?\r

The Intellectual Property Government Open Data (IPGOD) includes over 100 years of registry data on all intellectual property (IP) rights administered by IP Australia. It also has derived information about the applicants who filed these IP rights, to allow for research and analysis at the regional, business and individual level. This is the 2019 release of IPGOD.\r \r \r

How do I use IPGOD?\r

IPGOD is large, with millions of data points across up to 40 tables, making them too large to open with Microsoft Excel. Furthermore, analysis often requires information from separate tables which would need specialised software for merging. We recommend that advanced users interact with the IPGOD data using the right tools with enough memory and compute power. This includes a wide range of programming and statistical software such as Tableau, Power BI, Stata, SAS, R, Python, and Scalar.\r \r \r

IP Data Platform\r

IP Australia is also providing free trials to a cloud-based analytics platform with the capabilities to enable working with large intellectual property datasets, such as the IPGOD, through the web browser, without any installation of software. IP Data Platform\r \r

References\r

\r The following pages can help you gain the understanding of the intellectual property administration and processes in Australia to help your analysis on the dataset.\r \r * Patents\r * Trade Marks\r * Designs\r * Plant Breeder’s Rights\r \r \r

Updates\r

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Tables and columns\r

\r Due to the changes in our systems, some tables have been affected.\r \r * We have added IPGOD 225 and IPGOD 325 to the dataset!\r * The IPGOD 206 table is not available this year.\r * Many tables have been re-built, and as a result may have different columns or different possible values. Please check the data dictionary for each table before use.\r \r

Data quality improvements\r

\r Data quality has been improved across all tables.\r \r * Null values are simply empty rather than '31/12/9999'.\r * All date columns are now in ISO format 'yyyy-mm-dd'.\r * All indicator columns have been converted to Boolean data type (True/False) rather than Yes/No, Y/N, or 1/0.\r * All tables are encoded in UTF-8.\r * All tables use the backslash \ as the escape character.\r * The applicant name cleaning and matching algorithms have been updated. We believe that this year's method improves the accuracy of the matches. Please note that the "ipa_id" generated in IPGOD 2019 will not match with those in previous releases of IPGOD.