Molecular Operating Environment

The Molecular Operating Environment was developed by the Chemical Computing Group under the supervision of President/CEO Paul Labute.{{Cite web |last1=Frumkin |first1=Daniel |last2=Gayle |first2=Amy Tomlinson |last3=Faraguna |first3=Nico |last4=English |first4=Jen |last5=Sewell |first5=Dawson |last6=Namachunskiy |first6=Rostuslav |last7=Pettitt |first7=Katrina-Kay |last8=Scherfner |first8=Erin |last9=Mešanović |first9=Mevludin |title=Chemical Computing Group - Wiki |url=https://golden.com/wiki/Chemical_Computing_Group-D66VJA |access-date=2022-12-07 |website=Golden |language=en}} Founded in 1994{{Cite web |title=Chemical Computing Group Company Profile: Funding & Investors {{!}} PitchBook |url=https://pitchbook.com/profiles/company/58346-47 |access-date=2022-11-08 |website=pitchbook.com |language=en}} and based in Montreal, Quebec, Canada, this private company is dedicated to developing computation software that will challenge, revolutionize, and aid in the scientific methodology. The Chemical Computing Group contains a team of mathematicians, scientists, and software engineers constantly altering and updating MOE in order to improve the fields of theoretical/computational chemistry and biology, molecular modeling, and computer-driven molecular design.{{Cite web |last=Chemical Computing Group |date=November 7, 2022 |title=Molecular Operating Environment Products |url=https://www.chemcomp.com/Products.htm |access-date=November 7, 2022 |website=chemcomp.com}} Researchers specializing in pharmaceutics (drug-discovery); computational chemistry; biotechnology; bioinformatics; cheminformatics; molecular dynamics, simulations, and modeling are the main clients of the Chemical Computing Group.

As discussed before, MOE is a versatile software with main applications in 3D molecular visualization; structure-based protein-ligand design; antibody and biologics design, structure-based protein engineering; SAR and SPR visualization; ligand-based design; protein, DNA/RNA modeling; virtual screening; 3D pharmacophore screening; fragment-based discovery; structural bioinformatics; molecular mechanics and dynamics; peptide modeling; structural biology; cheminformatics and QSAR.

File:Molecular_Modeling.png

Molecular modeling and simulations is a process often used in computational chemistry, but there is wide application for researchers in a variety of fields. This theoretical approach allows scientists to extensively study the properties of molecules, and using the data can provide insight into how these molecules may behave in biological and/or chemical systems.{{Cite web |title=Molecular Simulation - an overview {{!}} ScienceDirect Topics |url=https://www.sciencedirect.com/topics/materials-science/molecular-simulation |access-date=2022-11-08 |website=www.sciencedirect.com}} This information is vital to the design of new materials and chemicals.

Molecular docking is a computation study used to primarily analyze the binding affinity of a ligand and a receptor. Often times, proteins are studied using this technique, because data from molecular docking allows scientists to predict if a ligand will bind to a specific molecule and if so, how strongly.{{Cite journal |last1=Meng |first1=Xuan-Yu |last2=Zhang |first2=Hong-Xing |last3=Mezei |first3=Mihaly |last4=Cui |first4=Meng |date=2011-06-01 |title=Molecular Docking: A powerful approach for structure-based drug discovery |journal=Current Computer-Aided Drug Design |volume=7 |issue=2 |pages=146–157 |doi=10.2174/157340911795677602 |issn=1573-4099 |pmc=3151162 |pmid=21534921}} Molecular docking can be used to predict the binding mode of already known ligands and/or novel ligands, and as a binding affinity predictive instrument.{{Cite journal |last1=Bartuzi |first1=Damian |last2=Kaczor |first2=Agnieszka A. |last3=Targowska-Duda |first3=Katarzyna M. |last4=Matosiuk |first4=Dariusz |date=2017-02-22 |title=Recent Advances and Applications of Molecular Docking to G Protein-Coupled Receptors |journal=Molecules |volume=22 |issue=2 |pages=340 |doi=10.3390/molecules22020340 |issn=1420-3049 |pmc=6155844 |pmid=28241450|doi-access=free }} Binding affinity is measured by the change in energy and the more negative the energy, the more stable the complex and the tighter the ligand binds to the receptor.{{Cite journal |last1=Kastritis |first1=Panagiotis L. |last2=Bonvin |first2=Alexandre M. J. J. |date=2013-02-06 |title=On the binding affinity of macromolecular interactions: daring to ask why proteins interact |journal=Journal of the Royal Society Interface |volume=10 |issue=79 |pages=20120835 |doi=10.1098/rsif.2012.0835|pmid=23235262 |pmc=3565702 }} Data from molecular docking can be used to construct new compounds that are more or less efficient at binding to a specific molecule. Molecular docking is extensively used throughout drug discovery for these reasons.{{Cite journal |last1=Pinzi |first1=Luca |last2=Rastelli |first2=Giulio |date=2019-09-04 |title=Molecular Docking: Shifting Paradigms in Drug Discovery |journal=International Journal of Molecular Sciences |volume=20 |issue=18 |pages=4331 |doi=10.3390/ijms20184331 |issn=1422-0067 |pmc=6769923 |pmid=31487867|doi-access=free }}

File:Docking_representation_2.png

Preparing for molecular docking studies can involve many steps. When docking proteins, proteins are obtained from the Protein Data Bank (PDB), which is an online, open access resources containing the classification, structure/folding, organism, sequence length, mutations, genome, sequence, and other data relating to proteins.{{Cite web |last=Bank |first=RCSB Protein Data |title=RCSB PDB: Homepage |url=https://www.rcsb.org/ |access-date=2022-11-08 |website=www.rcsb.org |language=en-US}} The structure of a protein can precisely be determined through a process known as X-ray crystallography. This process involves a concentrated beam of X-rays that is directed at a crystal.{{Cite journal |last1=Smyth |first1=M S |last2=Martin |first2=J H J |date=February 2000 |title=x Ray crystallography |journal=Molecular Pathology |volume=53 |issue=1 |pages=8–14 |doi=10.1136/mp.53.1.8 |issn=1366-8714 |pmc=1186895 |pmid=10884915}} When X-rays are projected to a crystal structure, the crystal diffracts the X-rays in specific directions.{{Cite web |title=X-Ray Crystallography - an overview {{!}} ScienceDirect Topics |url=https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/x-ray-crystallography |access-date=2022-11-08 |website=www.sciencedirect.com}} These directions allow scientists to map and determine the detailed structure of proteins, which is then recorded and uploaded to the PDB.{{Cite web |date=2013-10-02 |title=X-ray Crystallography |url=https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Supplemental_Modules_(Analytical_Chemistry)/Instrumentation_and_Analysis/Diffraction_Scattering_Techniques/X-ray_Crystallography |access-date=2022-11-08 |website=Chemistry LibreTexts |language=en}}

The protein structure file is downloaded from the PDB and opened in a molecular docking software. There are many programs that can facilitate molecular docking such as AutoDock, DOCK, FlexX, HYDRO, LIGPLOT, SPROUT, STALK,{{Cite web |title=6.List of softwares used in molecular docking - Molecular Docking |url=https://sites.google.com/site/moleculardocking123/list-of-softwares-used-in-molecular-docking |access-date=2022-11-08 |website=sites.google.com}} and Molegro Virtual Docker.{{Cite journal |last1=Pagadala |first1=Nataraj S. |last2=Syed |first2=Khajamohiddin |last3=Tuszynski |first3=Jack |date=2017-01-16 |title=Software for molecular docking: a review |journal=Biophysical Reviews |volume=9 |issue=2 |pages=91–102 |doi=10.1007/s12551-016-0247-1 |issn=1867-2450 |pmc=5425816 |pmid=28510083}} Alternatively, some protein structures have not been experimentally determined through the use of X-ray crystallography and therefore, are not found on the PDB. In order to produce a protein molecule that can be used for docking, scientists can use the amino acid sequence of a protein and a program named UniProt to find protein structures in the PDB that have similar amino acid sequences.{{Cite web |title=UniProt |url=https://www.uniprot.org/ |access-date=2022-11-08 |website=www.uniprot.org}} The amino acid sequence of the protein that is being constructed is then used in combination with the protein structure found in the PDB with the highest percent similarity (template protein) in order to create the target protein used in docking. Although this method does not produce an exact model of the target protein, it allows scientists to produce the closest possible structure in order to conduct computational methods and gain some insight into the behavior of a protein. After constructing the necessary molecules for docking, they are imported into a computational docking software such as MOE. In this program, proteins can be visualized and certain parts of the molecule can be isolated in order to obtain more precise data for a region of interest. A cavity, or region where the molecular docking will take place, is set around the binding site, which is the region in the receptor protein where the ligand attaches to. After specifying the cavity, molecular docking settings are configured and the program is run in order to determine the binding energy of the complex.

File:Cudeposition.gif

Molecular dynamic simulations is a computational study that predicts the movement of every atom in a molecule over time.{{Cite journal |last1=Hollingsworth |first1=Scott A. |last2=Dror |first2=Ron O. |date=2018-09-19 |title=Molecular dynamics simulation for all |journal=Neuron |volume=99 |issue=6 |pages=1129–1143 |doi=10.1016/j.neuron.2018.08.011 |issn=0896-6273 |pmc=6209097 |pmid=30236283}} Molecular dynamics can evaluate the movement of water, ions, small and macromolecules, or even complex systems which is extremally useful for reproducing the behavior of chemical and biological environments.{{Cite journal |last1=Hernández-Rodríguez |first1=Maricarmen |last2=Rosales-Hernández |first2=Martha C. |last3=Mendieta-Wejebe |first3=Jessica E. |last4=Martínez-Archundia |first4=Marlet |last5=Basurto |first5=José Correa |date=2016 |title=Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design |url=https://pubmed.ncbi.nlm.nih.gov/27237821/#:~:text=Molecular%20Dynamics%20(MD)%20simulations%20is,water%20molecules%20and%20lipid%20membranes |journal=Current Medicinal Chemistry |volume=23 |issue=34 |pages=3909–3924 |doi=10.2174/0929867323666160530144742 |issn=1875-533X |pmid=27237821}} This theoretical approach allows scientists to gain further insight into how molecules may behave with respect to each other, specifically if a molecule will leave or remain in a binding pocket. If a molecule remains in a binding pocket, this often indicates that the molecule creates a stable complex with the receptor and is energetically favorable.{{Cite web |title=Molecular Dynamics - an overview {{!}} ScienceDirect Topics |url=https://www.sciencedirect.com/topics/earth-and-planetary-sciences/molecular-dynamics |access-date=2022-11-09 |website=www.sciencedirect.com}} On the other hand, if the molecule leaves the binding pocket, this indicates that the complex is not stable. This information is then utilized to design new compounds with characteristics that may have a greater or lesser affinity for a receptor.

File:Drug_discovery_cycle_2.png

Drug discovery is a process that involves the use of computational, experimental, and clinical studies in order to design new therapeutics.{{Cite journal |last1=Zhou |first1=Shu-Feng |last2=Zhong |first2=Wei-Zhu |date=2017-02-13 |title=Drug Design and Discovery: Principles and Applications |journal=Molecules |volume=22 |issue=2 |pages=279 |doi=10.3390/molecules22020279 |issn=1420-3049 |pmc=6155886 |pmid=28208821|doi-access=free }} This process is lengthy and costly, yet it is the most popular process to date in developing successful treatments and medicines for a variety of diseases. The increasing use of drug discovery can be attributed to new technology that allow for computation/theoretical studies. Data from computation/theoretical studies is often the foundation and reasoning for the development of new drugs.{{Cite web |title=Drug Development - an overview {{!}} ScienceDirect Topics |url=https://www.sciencedirect.com/topics/nursing-and-health-professions/drug-development |access-date=2022-11-08 |website=www.sciencedirect.com}} Without promising theoretical data, these compounds may not be synthesized and tested during experimental studies. Molecular modeling, molecular docking, and MD simulations are some of many computation studies that takes places during drug discovery, allowing scientists to thoroughly study the structure and properties of organic and inorganic molecules. By studying these properties, scientists can gain insight to predict the affinity of molecules in biological and chemical systems in order to determine how a therapeutic may react with different types of chemicals, receptors, and other conditions found in humans or other animals. For example, molecular dynamics is often used throughout drug discovery in order to identify structural cavities that are important for determining binding affinity. This data is then compiled and analyzed to determine if certain therapeutics should be synthesized and tested clinically, or if further optimization is required for the design of new medicines that are more effective.{{Cite web |title=Drug discovery - Latest research and news {{!}} Nature |url=https://www.nature.com/subjects/drug-discovery |access-date=2022-11-08 |website=www.nature.com}}

Computational chemistry can also be applied to the development of safer pesticides and herbicides. Recently, the increasing use of pesticides and herbicides has raised much controversy due to environmental and public health concerns. It was found that although these chemicals are designed to kill target pests, its effects can often harm other organisms, humans included.{{Cite web |title=Pesticides & Human Health {{!}} Californians for Pesticide Reform |url=https://www.pesticidereform.org/pesticides-human-health/ |access-date=2022-11-10 |language=en-US}} Some types of pesticides and herbicides such as organophosphates and carbamates can affect the nervous system in humans, while others were found to be carcinogenic, irritate the skin or eyes, and even affect the hormone or endocrine system.{{Cite web |last=US EPA |first=OCSPP |date=2015-08-11 |title=Human Health Issues Related to Pesticides |url=https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/human-health-issues-related-pesticides |access-date=2022-11-09 |website=www.epa.gov |language=en}} Furthermore, neonicotinoids is another type of pesticide that recently gained popularity due to its effectiveness at targeting aphids and other pests that hinder agriculture production.{{Cite web |last1=May 25 |last2=Lindwall |first2=2022 Courtney |title=Neonicotinoids 101: The Effects on Humans and Bees |url=https://www.nrdc.org/stories/neonicotinoids-101-effects-humans-and-bees |access-date=2022-11-09 |website=NRDC |language=en}} Although there are not many human health concerns associated with neonicotinoids (which is another reason for its popularity), the increasing use of this pesticide has been linked to Colony Collapse Disorder (CCD), or the rapid disappearance of adult bees.{{Cite web |last1=Boston |first1=677 Huntington Avenue |last2=Ma 02115 +1495‑1000 |date=2014-05-09 |title=Study strengthens link between neonicotinoids and collapse of honey bee colonies |url=https://www.hsph.harvard.edu/news/press-releases/study-strengthens-link-between-neonicotinoids-and-collapse-of-honey-bee-colonies/ |access-date=2022-11-10 |website=News |language=en-us}} Due to this pattern, the European Union has banned the outdoor use of three neonicotinoid pesticides in an attempt to mitigate CCD.{{Cite web |title=European Union expands ban of three neonicotinoid pesticides |url=https://www.science.org/content/article/european-union-expands-ban-three-neonicotinoid-pesticides |access-date=2022-11-10 |website=www.science.org |language=en}} Clearly, there are multiple issues regarding the use of these pesticides and herbicides. A call for safer and more efficient pesticides and herbicides is being accomplished with the help of computational/theoretical methods.

File:Protein_folding_figure.png

Computational/theoretical chemistry and biology methods are continuously pushing the horizon. Recently, DeepMind, which is a company specializing in the development of artificial intelligence (AI), created an AI system named AlphaFold.{{Cite web |title=AlphaFold Protein Structure Database |url=https://alphafold.ebi.ac.uk/ |access-date=2022-11-10 |website=alphafold.ebi.ac.uk}} AlphaFold is the most advanced system to date that can accurately predict a protein's 3D structure from its amino acid sequence.{{Cite journal |last1=Jumper |first1=John |last2=Evans |first2=Richard |last3=Pritzel |first3=Alexander |last4=Green |first4=Tim |last5=Figurnov |first5=Michael |last6=Ronneberger |first6=Olaf |last7=Tunyasuvunakool |first7=Kathryn |last8=Bates |first8=Russ |last9=Žídek |first9=Augustin |last10=Potapenko |first10=Anna |last11=Bridgland |first11=Alex |last12=Meyer |first12=Clemens |last13=Kohl |first13=Simon A. A. |last14=Ballard |first14=Andrew J. |last15=Cowie |first15=Andrew |date=August 2021 |title=Highly accurate protein structure prediction with AlphaFold |journal=Nature |language=en |volume=596 |issue=7873 |pages=583–589 |doi=10.1038/s41586-021-03819-2 |pmid=34265844 |pmc=8371605 |bibcode=2021Natur.596..583J |issn=1476-4687}} The protein folding problem first began to emerge around the 1960s and ever since, scientists have struggled in determining methods to precisely predict the way a protein will fold solely based on the amino acid sequence.{{Cite journal |last1=Dill |first1=Ken A. |last2=Ozkan |first2=S. Banu |last3=Shell |first3=M. Scott |last4=Weikl |first4=Thomas R. |date=2008-06-09 |title=The Protein Folding Problem |journal=Annual Review of Biophysics |volume=37 |pages=289–316 |doi=10.1146/annurev.biophys.37.092707.153558 |issn=1936-122X |pmc=2443096 |pmid=18573083}} However, with recent advances in technology, AlphaFold has made a breakthrough in this long lasting issue. By utilizing a database with over 350,000 structures, AlphaFold can determine the shape of a protein in a few minutes with atomic accuracy.{{Cite web |title=AlphaFold |url=https://www.deepmind.com/research/highlighted-research/alphafold#:~:text=These%20sequences%20are%20assembled%20according,of%20a%20protein%27s%203D%20structure. |access-date=2022-11-10 |website=www.deepmind.com |language=en}} The ability to predict the structure of millions of unknown proteins can help to combat disease, find more effective medicines, and unlock other unknowns that govern life. This technological breakthrough will revolutionize future research and will have profound effects for the scientific community.

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