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These gaps create maintain a predefined alignment. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620169192872-W2VX0W9TOX4LDEUSZKN5/Sequences_5.PNG Resources - Sequence Formats for SARvision https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620151172541-7DJ92E5E489Z8RU0JGBP/Sequences_4.PNG Resources - Sequence Formats for SARvision https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620281635553-XO3TVP12962I2RI5I6E9/Sequences_6.PNG Resources - Sequence Formats for SARvision https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620147984647-PNBIWMDPQUWOGBPNRTV9/Sequences_1.PNG Resources - Sequence Formats for SARvision Example of FASTA format in Excel:*.csv format. Additional data can be added to the file for import. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620149906074-MRGNCLQTN5XE2XYTBPG3/Sequences_2.PNG Resources - Sequence Formats for SARvision Modified FASTA format where a modifier (optional: not often used) is in red, crosslinks between and within chains are numbered and colored in blue and finally brackets enclose multi-letter monomers. Note that single letter monomer (‘L’, ‘P’ and ‘T’) may use brackets or not. The inclusion of a few features greatly expands the chemistry in a FASTA format while maintaining its simplicity. https://www.chemapps.com/resources/subsets monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620142648681-GF0JO6OCJSIB0D5HGXPE/Subsets_th.PNG Resources - Working with Subsets Create interactive controls to filter sequence alignment tables. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620105176416-9NQHFUH1I5ZOKJ0H8KTU/Subsets_2.PNG Resources - Working with Subsets The invariant map is used to interactively build sequence motifs to filter the sequence table. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620103984068-F1PSWIMJL4W7X5UZ302K/Subsets_1.PNG Resources - Working with Subsets The Scatter plot can separate data on two activity axes. Selection of one set of points is used to filter the sequence table to only those sequences selected. https://www.chemapps.com/resources/antibodies monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619890178672-33AJMGRHB5EMVRUHT4B4/AB_th.PNG Resources - Studying Sequence Activity Relationships in Antibodies Sequence alignment table of a series of Antibodies’ light chain CDR1 domains. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620076423765-MKSU2GHHUIRWQ7HU99TY/AB_1.PNG Resources - Studying Sequence Activity Relationships in Antibodies Thirty-six anti-HIV antibodies arranged from most potent to least potent. The sequence alignment is filtered to study only the 3 CDRs from the light chain. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620084314243-GIVW9L2PFOABEQUH9GG2/AB_2.PNG Resources - Studying Sequence Activity Relationships in Antibodies Import antibody sequences and data into SARvision to create sequence analysis tables. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620141894981-VLB6HRLFDRC8IZCKJOFV/AB_3.PNG Resources - Studying Sequence Activity Relationships in Antibodies An example input file with antibody sequences and data. https://www.chemapps.com/resources/mutation-sets monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619830560663-11SOADVOKIWGJX5FG6OO/Mutation_Set_th.PNG Resources - Using Mutation Sets to identify Key Residues A mutation set shows Sequence Activity Relationships for a specific position. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619829330073-ZXW9HNIPHSF6H38JFQMB/Mutation_Set1.PNG Resources - Using Mutation Sets to identify Key Residues Select a sequence alignment position to study, one at a time. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619829913784-KPMGTFR6ESKYPVHZRKM5/Mutation_Set2.PNG Resources - Using Mutation Sets to identify Key Residues A mutation set is a family of sequences that vary at a single position, but are otherwise identical. Sequence Activity Relationships can be clearly observed in these sequence subsets. https://www.chemapps.com/resources/monomer-table monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619807744260-357TTDVGFGUPLCP1NT5K/Monomer_table_th.PNG Resources - How to Prepare Monomer Tables for Biologics Research In sequence analysis, every monomer has a structure and associated data to help elucidate Sequence Activity Relationships. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619828640422-27OV29AS1VD2WIKAC0DW/Monomer_table_5.PNG Resources - How to Prepare Monomer Tables for Biologics Research A simple modifier table contains annotations to describe modified positions. Modifier tables are not used often. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619807854740-B6H4CRKKI0JZVWSXSBWT/Monomer_table_1.PNG Resources - How to Prepare Monomer Tables for Biologics Research Column field descriptions: The SMILES column contains a smiles string that encodes the chemical structure of the monomer. The column is necessary, but the individual entries can be empty. Note that Smiles strings can be generated for molecules using any chemically aware spreadsheet program (such as SARvision|SM). Three name columns that contain a short, medium and long name. These are used interchangeably inside SARvision|Biologics to optimize the look of tables and views. Typically, the ‘SHORT_NAME’ is the smallest possible abbreviation, ideally 1-2 letters, the ‘MEDIUM_NAME’ designates a 3-4 letter abbreviation similar to those used in the PDB and last is the ‘LONG_NAME’ which encodes the formal name for a residue. Examples would be short: F, medium: PHE: and long: L-phenylalanine. The SYNONYMS field contains any other names used for the same residue separated by semicolons. This is used in sequence parsing to consolidate naming conventions used in disparate research groups. An example would be: PHE;Phe; F to designate a phenylalanine. This is a great way to normalize names without having to edit all the sequences that have been generated. CLUSTAL_SUBSTITION contains the closest natural residue (e.g. ‘p-fluoro-phenylalanine’ most similar to ‘F’). This is used as a substitution when performing alignments that employ algorithms that use PAM and Blossum matrices. CATEGORY is an allows for an arbitrary designation of a monomers. It could be any text useful for categorizing residues such as ‘aromatic’, ‘polar’, ‘lippophilic’, ‘warhead’ or null. In several views these are used to group monomers into groups. The FONT_COLOR is the color of the font for this residue in the program. These are usually black with red, blue, green…. To designate unnatural or otherwise interesting residues. Note that RGB(##,##,##) can be used instead of the common color names. The SORTORDER column is a real number tells the program how to sort residues. These numbers are completely arbitrary and left to the user’s discretion. An example would be Phe:10, D-Phe: 10.01, p-F-Phe:10.02, m-F-Phe: 10.03, m-methyl-Phe: 10.04, N-methyl-Phe: 10.05, Tyr: 11 which when sorted would group the phenylalanine residues together and arrange them by substitution pattern on the phenyl ring. The DATA:ColumnName are data columns. There can be an arbitrary number of columns that contain numeric data that describes the monomer and may be useful for analysis. Note that SARvision|Biologics automatically adds a number of rdkit calcuated properties by default. Note that early versions of SARvision used “<DATA>” instead of the “DATA:” designation in the name field. This is still recognized, however, the named using “DATA:” is database friendly and recommended. The BKG:ColumnName are coloring columns that when applied color the background in the alignment table. There can be an arbitrary number of columns that can contain colors. Note that colors are defined using RGB color coding but it can recognize simple names such as ‘blue’, ‘green’, ‘red’… Note that SARvision|Biologics automatically adds a number of rdkit calcuated properties by default. Note that early versions of SARvision used “<BKG>” instead of the “BKG:” designator in the name field. This is still recognized, however, the named using “BKG:” is database friendly and recommended. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619826977439-AI3XX8IXF236ED70APDA/Monomer_table_31.PNG Resources - How to Prepare Monomer Tables for Biologics Research Monomer tables can be stores as a file locally, in Oracle or in CDDVault. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619808483372-RAQK7ICGM29LN1L4VTYR/Monomer_table_2.PNG Resources - How to Prepare Monomer Tables for Biologics Research The molecular spreadsheet in SARvision|SM can be used to help create residue tables. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619809174179-53DBEFM3LCOB22YYCO21/Monomer_table_3.PNG Resources - How to Prepare Monomer Tables for Biologics Research Example of monomer data and coloring used to make the sequence table intuitive with a greater depth of information. https://www.chemapps.com/resources/mutation-cliff monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619583334874-CKZ575W8K7HVA0EAOPKT/MutationCliff_th.PNG Resources - Finding Key Residues using Mutation Cliffs Mutation cliffs identify pairs of sequences where only a single residue is modified and then correlates this change to changes in activity. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1621631282635-DMZY5BW4C7QMGKZF4ET5/MutationCliff_1.PNG Resources - Finding Key Residues using Mutation Cliffs A mutation cliff in which 9 pairs of sequences that differ at only a single position and mutate that position A->?. These pairs are summarized in the inset table at the right. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619720033858-HFPRXGUPIGN7K4IB63LN/MutationCliff_2.PNG Resources - Finding Key Residues using Mutation Cliffs An interactive mutation cliff allows the user to interactively analyze pairs of sequences that differ at only a single position. https://www.chemapps.com/resources/invariant-map monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619577293153-6TOYIIH5Q0J0MWYLYFP7/Invariant+Map_th.PNG Resources - Use Invariant Maps to Identify Important Monomers in Sequence Analysis An Invariant map displays groups of sequences based on monomer substitution patterns at each position. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619571647452-WVZPNF4SPMVXHV5NC89P/Invariant+Map_1.PNG Resources - Use Invariant Maps to Identify Important Monomers in Sequence Analysis The table displays an invariant map for a set of Somatostatin analogs. The heat-mapping depicts aggregate activity against the SST2 receptor. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619577083398-4IBIZUU6W1DA1WGO3AIB/Invariant+Map_2.PNG Resources - Use Invariant Maps to Identify Important Monomers in Sequence Analysis An interactive invariant map (bottom) is used to create subset of sequences to be display in an alignment table (top). Selection of the 6 alanines in the 7 position triggers the sequence table to show only the 6 sequences that have alanine (A) in the 7 position. https://www.chemapps.com/resources/logoplot monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619571197099-413D69CWBS2WSH8GN5BI/logo_th.PNG Resources - Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships A logo plot highlights residues that are important by scaling font size with activity. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619570768760-RDJIAXH17TG4KFSR0AMQ/logo_3.PNG Resources - Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships Fly overs slice the chart by position to show a plot of each residue at that position. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619740619802-MMOA679NRTVQ741LWXU2/logo_4.PNG Resources - Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships Using a subset filter, logo plots can be built t represent specific activity profiles. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619570744827-EZ55ADEMJQK7ZR9P0VRE/logo_2.PNG Resources - Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships The Sequence bar plot can be displayed as letters or solid bars. The Y-axis can be counts or any data field modified and aggregated by average, min or max. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619570712746-026I6U2WKPRPRMIZH9XY/logo_1.PNG Resources - Using Sequence Logo and Bar Plots to Study Sequence Activity Relationships A sequence logo plot can display sequence motifs that define a biological activity. https://www.chemapps.com/resources/dendrogram monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619542144317-WTXOG1PQR611WPNTFAL8/Dendogram_th.PNG Resources - Using Dendrograms in Biologics Research Dendrograms are an excellent way to cluster sequences by similarity or data to visualize Sequence Activity Relationships. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619657026609-XS42JPPO5PZ9IWRJJAT3/Dendrogram_4.PNG Resources - Using Dendrograms in Biologics Research Interactive highlighting of sequences in the Dendrogram using range filters. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619543616922-0X1YOG28W0K13RPQ2PP0/Dendrogram_2.PNG Resources - Using Dendrograms in Biologics Research Dendrogram depicting Somatostatin analogs grouped by sequence activity to SST4 receptor. The dendrogram looks markedly different to the tree built using sequence identity. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619543594417-U2R90FAVLGUEE28SGZ22/Dendrogram_1.PNG Resources - Using Dendrograms in Biologics Research Dendrogram depicting Somatostatin analogs grouped by sequence identity. Note the ‘Cluster by’ drop down allows selection by the user of any data to build dendrograms of sequences on demand. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619543686864-P6WJ3IPSBORERQ6PRB3J/Dendrogram_6.PNG Resources - Using Dendrograms in Biologics Research An interactive display can be set up to filter Sequence tables by selection in the Dendrogram view. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619543639873-HL52JSZ5CJONJ5TRBGEN/Dendrogram_3.PNG Resources - Using Dendrograms in Biologics Research Dendrogram with a heat-map illuminating pockets of activity against the SST2 receptor. https://www.chemapps.com/resources/sequence-activity-relationships monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618452014975-HZK9YGW53NB1LSHCTFWA/SeqAR_thumb.PNG Resources - Sequence Activity Relationships Sequence Activity Relationships are akin to Structure Activity Relationships except they are studied in sequence space. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618522324143-IP7LN5UNZ01VBQR65KH5/SeqAR_1.PNG Resources - Sequence Activity Relationships A sequence alignment table with activity data that can be used to study Sequence Activity Relationships. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618522353617-7AS0Z1J1VD7YVGOECDYD/SeqAR_2.PNG Resources - Sequence Activity Relationships Columns in a sequence alignment correspond to positions on the 3D molecule that have functional significance to the activity of the compound. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618553959100-FESG7KE3W3MX351WG4ZZ/SeqAR_3.PNG Resources - Sequence Activity Relationships An example monomer table used to study Sequence Activity Relationships. Each row adds a dimension of data to a monomer in the sequence to facilitate pharmacological analysis. https://www.chemapps.com/resources/sequences-cddvault monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618017327662-OMC5FOQXWA3AZGTD6INA/CDD_SM1.PNG Resources - Analyzing Sequences from CDDVault https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619754248526-ORU3RFHMBL1TLINHBLHM/Seq_CDDVault_2.PNG Resources - Analyzing Sequences from CDDVault https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619758236042-SGGD46H967BYP1W7VES6/Seq_CDDVault_3.PNG Resources - Analyzing Sequences from CDDVault https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1619754220908-2PF73VVBJC7DDAVK1UD4/Seq_CDDVault_1.PNG Resources - Analyzing Sequences from CDDVault https://www.chemapps.com/resources/svsm-cddvault monthly 0.5 2022-04-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618020706623-GG77NKVDNNPLY1ESWZCR/CDD_SM3.PNG Resources - Analyzing Molecules from CDDVault https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618017327662-OMC5FOQXWA3AZGTD6INA/CDD_SM1.PNG Resources - Analyzing Molecules from CDDVault https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1618017350349-VZJ2ULZBKXTQFSWZPWMM/CDD_SM2.PNG Resources - Analyzing Molecules from CDDVault https://www.chemapps.com/resources/protacs monthly 0.5 2022-04-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/296d6f84-03ec-47b1-88e8-a8327fb97446/PROTAC.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out Performing SAR analysis on bi-ligands such as PRTOACS requires tools that can identify the linker and break the molecule into its constituent parts. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/ea6d2430-2f9c-4073-81d1-a3a338970905/PROTAC_MOLECULAR_PAIR.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out PROTACS are broken into molecular pairs on each row based on changes in only one of the ligands or the linker. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/c843bd03-f251-479b-a001-23af909003be/PROTAC_PROPERTIES.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out A number of properties can be calculated for each PROTAC, each ligand in the PROTAC molecule and for the linker. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/ba75bdad-f0a0-485e-bf25-766656fa44e4/PROTAC_SAR_BUTTON.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/deb36329-b4e4-4d01-b119-d85e998f8048/PROTAC_RGROUP.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out The R-Group table breaks the PROTAC molecules into the constituent parts and places these into R1, R2 and Linker columns. This table can be sorted, heat-mapped and filtered to facilitate SAR analysis. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/39400899-f101-49b6-a97b-2e35c82b39b5/OpenPROTAC_BCR-ABL.PNG Resources - Analysing PROTAC Structure-Activity Relationships - Make it stand out Molecules in SDF or smiles format can be easily imported into SARvision|SM (file->import molecles : loads SDF, Smiles). A set of molecules designed to degrade BCR-ABL can be loaded for study (download here). We are using a set obtained from PROTAC DB: Nucleic Acids Research, 2020. Doi: 10.1093/nar/gkaa807 for this example. https://www.chemapps.com/resources/find-molecules monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/84837bf7-4368-4bc2-b96f-3b5ef054c9b1/MoleculeFinder_th.png Resources - Finding Molecules Online The CHEMAPPS search page shows results for substructure searches of vendor and other online molecules. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/ef90dcad-b01b-4b43-a2e0-2881de062d57/MoleculeFinder_Cart.PNG Resources - Finding Molecules Online The cart contains collections of molecules created by the user. These display some relevant chemical information. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/41869236-951e-4f39-8c97-0a00181b8e70/MoleculeFinder_Search.PNG Resources - Finding Molecules Online The CHEMAPPS main search page where the user can search libraries of molecules by chemical type, substructure and application. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/6c874c51-35ec-4310-a514-1778d3f8ad50/MoleculeFinder_PopScaffolds.PNG Resources - Finding Molecules Online Each scaffold is grouped by chemical type and can be clicked to perform a search against a library of molecules. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/81d14aa0-a0c9-4afa-b6c6-cf427bb1b05a/MoleculeFinder_Results.PNG Resources - Finding Molecules Online Search page showing the selected scaffold (top), child scaffold families (middle) and molecule hits (bottom). Exact substructure matches are highlighted with blue squares. Below each molecule descriptive data is display such as the cas# in this case. https://www.chemapps.com/resources/hts-analysis monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616912921509-25EPOQFJ9YGZGRUOKAHI/tree_thumb.PNG Resources - Analyzing High Throughput Data Using Scaffold Trees and Data Grids A hierarchical scaffold tree intuitively organizes molecules based on structure. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616962057583-M4MKMW3TALJWITXN4NWM/tree_4.PNG Resources - Analyzing High Throughput Data Using Scaffold Trees and Data Grids HTS or activity data can be mapped onto the hierarchical scaffold tree to help isolate active molecules. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616961982955-DNCTX4Y774TI31JFW5ZV/tree_3.PNG Resources - Analyzing High Throughput Data Using Scaffold Trees and Data Grids A molecule grid of heat-mapped HTS data filter by scaffold structure or chemotype. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616913984631-C32MBBN3KQUVHXB8HLUI/tree_2.PNG Resources - Analyzing High Throughput Data Using Scaffold Trees and Data Grids A molecular grid of molecules displaying heat-mapped HTS data. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616965903692-C2TRQ7PMNOYSJRD5BEVM/tree_5.PNG Resources - Analyzing High Throughput Data Using Scaffold Trees and Data Grids https://www.chemapps.com/resources/data-grid monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616738892080-OI3IVGQ8TQBCMQF37LS8/DataGrid_thumb.PNG Resources - Molecule Data Grid A Molecule data grid is a nice compact way to show high density data. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616738400573-1255E92UAPTZR39YY1BT/DataGrid_1.PNG Resources - Molecule Data Grid A molecular data grid displays molecules and data in a nice compact form. https://www.chemapps.com/resources/sabre monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616734043105-I0HQYFDTCSBJN7KK424Y/SABRE_thumb.PNG Resources - Two-Way R-Group Tables A two-way R-Group table highlights key features in R-Group space. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616735738144-T36834KCNCI7HB8WINWS/SABRE_3.PNG Resources - Two-Way R-Group Tables The population of molecules in the two-way table can be filtered at any R-position to study only those with R-Groups that are relevant to the current analysis. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616735715451-6WSB3X5RSHWI9VCB8921/SABRE_1.PNG Resources - Two-Way R-Group Tables There are multiple two-way tables that can be built for a molecule set. Each represents a slice through N-dimensional R-Group space defined by a scaffold core. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616735658145-9KKKKBFIHAO8YOT2PG37/SABRE2.PNG Resources - Two-Way R-Group Tables Under the main menu are a series of dialogues that will build custom formatted two-way tables for SAR analysis. https://www.chemapps.com/resources/rgroup-table monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616722771851-O1T3CDD6MLOGFKUTYDZM/RT_1.PNG Resources - R-Group Tables R-Group tables are built on demand by double clicking on any scaffold. https://www.chemapps.com/resources/molecular-pairs monthly 0.5 2021-04-30 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616723708897-XUV8P40I2BYXCKZ38A6A/mp_thumb.PNG Resources - Scaffold Centered Molecular Pairs Molecular pairs are pairs of molecules that differ at only a single position. Isolating structural changes in this way useful to study Structure Activity Relationships. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616630988837-XUVC06NGAQVIS0K9Q4BU/MP_3.PNG Resources - Scaffold Centered Molecular Pairs Comparing scaffold cores or core-hopping is easily performed by using folders in the scaffold tree. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616630790613-5LKKN3D4J9FJMF15NF0X/MP_2.PNG Resources - Scaffold Centered Molecular Pairs SARvision builds molecular pair tables centered on specific scaffolds. Pairs can be easily filtered by R-position to facilitate analysis. https://www.chemapps.com/resources/molecule-spreadsheets monthly 0.5 2021-05-06 https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616689174881-3938T0ZRBU7FHRPZ26L0/MS_1.PNG Resources - Molecule Spreadsheets A typical molecule spreadsheet. Right click on row headers, spreadsheet header tab, column header and cells to get context menus to modify objects. Click on any data cell to modify or add data. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1620250975524-AABMA200OUF99MET8YP5/MS_3.PNG Resources - Molecule Spreadsheets Molecules cluster in related series based on scaffold substructure. Draw a scaffold and double click on it to filter, color code and align molecules to the selected scaffold for easy analysis. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616708252777-G1W4BWW4DCLPQZDB79CE/MS_4.PNG Resources - Molecule Spreadsheets Filter data by scaffold substructure and/or data ranges to see only relevant molecules in the spreadsheet. https://images.squarespace-cdn.com/content/v1/5ff64e7d2c86173b0bf31129/1616707300620-R9DA3KQT385JMCUEB8PG/MS_2.PNG Resources - Molecule Spreadsheets Molecular spreadsheets can be sorted, edited, heat-mapped and cells formatted to help identify trends in biological assay data. Under Data Table tab (right click) export to Excel/Word.