Dear Mohamed Nabeel Malash ,

Maybe These links can help you that what you are looking for:

https://www.uniprot.org/ . (this link we are using for to understand mutant genes-based enzymes for our projects and studies, so that this will be useful for your researches. Especially you can have many informations about proteins such as enzymes..)

https://www.expasy.org/resources/search/keywords:enzyme (this link is most useful because you can have relationship between metabolic patways and ezymes so you can study on metabolic pathway diseases.. expasy is very important tool for your all need such as Biochemistry and Molecular Biology relations.)

https://biokinet.belozersky.msu.ru/pocketzebra (this tool can help you as a it is the he latest bioinformatic procedures to detect Subfamily-specific positions (SSPs) implement entropy-based measures of subfamily-dependent distribution of amino acids, take into account sequence and structural information, physicochemical properties of amino acid side chains and perform ranking to automatically select the most statistically significant hotspots for further evaluation by this way you can improve your enzymes formulae.)

http://autodock.scripps.edu/resources/adt (this is for lingand-receptor interactions that you can find or create a new enzyme which can interact with its receptor or ligans. I mean you can use your enzyme in targeted therapies.. )

There are lots of bioinformatic tool for optimal temperature, optimal pH for enzymes activity, based on enzyme sequence or 3D structure.

How can you choose the most proper tool? There is a rewiev for this question that i suggested for you in the attachment (Suplatov,2014).

I hope all these informations help you.

Sincerely,

Mesut

Dear Mohamed Nabeel Malash ,

Perhaps this is close to what you are looking for:

Lin, H., Chen, W., & Ding, H. (2013). AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes. PloS one, 8(10), e75726.

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075726

Good luck!

Better you need to work on use of Response Surface Methodology (RSM) after identifying a few vital parameters of enzyme activity.

I agree with Shamsher. I don't think you can get around doing experiments.

You could try if your enzyme is in the BRENDA database (https://www.brenda-enzymes.org/). It lists all kind of parameters from published papers, including the things that interest you.

Chemical kinetics is about chemical reactions and there is no current way to predict how a chemical reaction will occur, unless you have some experimental information to start with and narrow down your options. Knowledge in this area is mostly experimental.

On the scale of complexity in the world of chemical kinetics, enzyme catalysis is at the top of the current challenges, predictions are ever harder to make.

So other than associations of sequence or structural similarities in enzyme families to the know properties, like the one noted by Rob Keller , are the most you will get, and they offer limiter certainty.

Take the suggestion by Achim Recktenwald and use BRENDA, and you may also find interesting data about structure and function in DJANGO, Pocket finder, F-pocket, caver, Q-site-finder and similar tools. You may find relatives of your enzyme and take their properties as an initial educated guess for your protein.

http://sfld.rbvi.ucsf.edu/django/

https://omictools.com/pocket-finder-tool

https://www.caver.cz/index.php?sid=133

http://fpocket.sourceforge.net/

Best wishes,

Rogelio

Great answer Rogelio!!

Thanks Achim Recktenwald ,

I appreciate it!

Many thanks dear Rob Keller for this paper. It is so valuable and can be a great tool, but their webserver is not working currently. It would be great if they kept it functional. It would have helped me greatly. If you know another similar webserver, please share it with me.

Many thanks dear Achim Recktenwald for your suggestion, but the enzyme I am working with is not yet on any databases or not even published. I still know nothing about its properties other than it is not soluble at neutral pH.

Great thanks dear Rogelio Rodríguez-Sotres for your great answer and effort in writing it. I have been going through the websites and webservers you kindly shared with me and they are good tools that at least may give me a hint by the homologous enzymes on them.

Great thanks dear Shamsher S. Kanwar for the notion of Response Surface Methodology which is new to me and I am getting to understand it and try to implement it as soon as I find any helpful properties about my enzyme.

Nice to see that you are increasing your research horizon and knowledge about working on enzymes.

This is in addition to some other relevant upstream fields. Thanks Dr Shamsher S. Kanwar.

Dear Mohamed Nabeel Malash ,

Maybe These links can help you that what you are looking for:

https://www.uniprot.org/ . (this link we are using for to understand mutant genes-based enzymes for our projects and studies, so that this will be useful for your researches. Especially you can have many informations about proteins such as enzymes..)

https://www.expasy.org/resources/search/keywords:enzyme (this link is most useful because you can have relationship between metabolic patways and ezymes so you can study on metabolic pathway diseases.. expasy is very important tool for your all need such as Biochemistry and Molecular Biology relations.)

https://biokinet.belozersky.msu.ru/pocketzebra (this tool can help you as a it is the he latest bioinformatic procedures to detect Subfamily-specific positions (SSPs) implement entropy-based measures of subfamily-dependent distribution of amino acids, take into account sequence and structural information, physicochemical properties of amino acid side chains and perform ranking to automatically select the most statistically significant hotspots for further evaluation by this way you can improve your enzymes formulae.)

http://autodock.scripps.edu/resources/adt (this is for lingand-receptor interactions that you can find or create a new enzyme which can interact with its receptor or ligans. I mean you can use your enzyme in targeted therapies.. )

There are lots of bioinformatic tool for optimal temperature, optimal pH for enzymes activity, based on enzyme sequence or 3D structure.

How can you choose the most proper tool? There is a rewiev for this question that i suggested for you in the attachment (Suplatov,2014).

I hope all these informations help you.

Sincerely,

Mesut

Thank you Dr. Mesut Karahan for these valuable resources. It will help certainly especially Pocketzebra and the review paper.

Mohamed Nabeel Malash I am happy for you. Please do not hesitate to contact with me that anything you want to ask for instance project collaborations... I am studying on designing new technologies about protein engineering, peptide vaccines, peptide drug, immune responses, stem cells, non coding RNAs...

Best wishes for your studies

Thank you dear Dr. Mesut Karahan . It will be an honor to me to collaborate with you in the areas of mutual interest and wish to be in contact with you. Thank you again for your kind reply.

Best wishes and warm regards

Those following this thread will find this paper enlightening:

https://science.sciencemag.org/content/364/6439/448.7

One step closer to the solution...

Best wishes

Rogelio

Thank you dear Dr. Rogelio Rodríguez-Sotres for sharing this valuable article. It will help a lot.

Best wishes and sincere regards

For optimal temperature, a paper came out shortly after you asked this question.

Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima

Article Machine Learning Applied to Predicting Microorganism Growth ...