| Antibody | Antibody PDB | Variant | Variant ID | RBD PDB | HADDOCK score | Van der Waals energy | Electrostatic energy | Desolvation energy | Restraints violation energy | Buried Surface Area |
|---|---|---|---|---|---|---|---|---|---|---|
| CC12.1 | 6XC2 | Alpha | B.1.1.7 | 6XC2 | -198.6 | -106.9 | -342.6 | -37.5 | 143.2 | 2778.5 |
| CC12.1 | 6XC2 | Beta | B.1.351 | 7VX1 | -171.9 | -93.9 | -298.1 | -33.1 | 147.3 | 2698.8 |
| CC12.1 | 6XC2 | Delta | B.1.617.2 | 7V7O | -178.8 | -100.2 | -290.8 | -33 | 125.3 | 2682.3 |
| CC12.1 | 6XC2 | Omicron | B.1.1.529 | 7T9J | -118.5 | -76.4 | -169.6 | -20.8 | 125.8 | 2121.4 |
| CC12.1 | 6XC2 | Omicron (Subvariant) | BA.2.75 | AlphaFold2 | -118.8 | -72.3 | -265.7 | -8.9 | 155.7 | 2265.6 |
| CC12.1 | 6XC2 | Omicron (Subvariant) | BA.5 | AlphaFold2 | -121.4 | -78 | -198.3 | -18.6 | 147.3 | 2326.3 |
Colby T. Ford colbyford
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colbyford
/ scipapers-chatgpt_articles.csv
Created
March 22, 2023 15:27
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| Title | URL | |
|---|---|---|
| Predictions of the SARS-CoV-2 Omicron Variant (B.1.1.529) Spike Protein Receptor-Binding Domain Structure and Neutralizing Antibody Interactions | https://www.frontiersin.org/articles/10.3389/fviro.2022.830202 | |
| An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies | https://www.nature.com/articles/s41591-021-01678-y | |
| Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution | https://www.nature.com/articles/s41586-022-05644-7 | |
| Substantial Neutralization Escape by SARS-CoV-2 Omicron Variants BQ.1.1 and XBB.1 | https://www.nejm.org/doi/10.1056/NEJMc2214314 | |
| ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5 | https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00010-5/fulltext |
colbyford
/ shiny_app_in_docker.Dockerfile
Created
October 25, 2022 18:40
Example Dockerfile for running a Shiny app in a container
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| # FROM rocker/shiny-verse:latest | |
| FROM rocker/shiny-verse:4.0.0 | |
| ## Install any Linux system dependencies | |
| RUN apt-get update && apt-get install -y \ | |
| sudo \ | |
| libcurl4-gnutls-dev \ | |
| libcairo2-dev \ | |
| libxt-dev \ | |
| libssl-dev |
colbyford
/ azure-databricks-with-vnet-and-nsg.json
Last active
July 13, 2022 14:13
ARM Template for deploying Azure Databricks with a VNet and Network Security Group
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| { | |
| "$schema": "https://schema.management.azure.com/schemas/2015-01-01/deploymentTemplate.json#", | |
| "contentVersion": "1.0.0.0", | |
| "parameters": { | |
| "location": { | |
| "type": "String", | |
| "defaultValue" : "eastus" | |
| }, | |
| "workspaceName": { | |
| "type": "String", |
colbyford
/ BA.2.75_BA.5_CC12.1_HADDOCK.md
Created
July 6, 2022 15:18
Comparison of CC12.1 antibody binding affinity of SARS-CoV-2 Omicron subvariants BA.2.75 and BA.5.
colbyford
/ pembrolizumab_vs_pemfauxlizumab_pd-1_binding.md
Created
June 8, 2022 00:22
Pembrolizumab vs. Pemfauxlizumab PD-1 Binding from HADDOCK
| PD-1 Binding | Pembrolizumab | Pemfauxlizumab |
|---|---|---|
| HADDOCK score | -138.0 +/- 0.8 | -60.6 +/- 4.2 |
| Van der Waals energy | -84.8 +/- 3.8 | -33.0 +/- 1.6 |
| Electrostatic energy | -232.2 +/- 25.9 | -292.2 +/- 32.7 |
| Desolvation energy | -7.8 +/- 1.6 | 18.5 +/- 2.8 |
| Restraints violation energy | 9.5 +/- 4.9 | 123.5 +/- 28.9 |
| Buried Surface Area | 2204.2 +/- 53.3 | 1678.7 +/- 60.2 |
colbyford
/ pembrolizumab_pemfauxlizumab_fabs.fasta
Last active
June 8, 2022 00:35
Comparison of Pembrolizumab and AlphaFold2-hallucinated "Pemfauxlizumab" Fab Sequences
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| >Pembrolizumab Light Chain | |
| EIVLTQSPATLSLSPGERATLSCRASKGVSTSGYSYLHWYQQKPGQAPRLLIYLASYLESGVPARFSGSGSGTDFTLTISSLEPEDFAVYYCQHSRDLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC | |
| >Pemfauxlizumab Light Chain | |
| PPTVTITPKHIHFDPGETFTVWATFSKPVYTDDGPKVKVYYRHPGGPYELLYKNATEKEPGWPDNIKTQYTGDRAWVTYDNMPECPHFYIYVRADVGGPPVWGKAVHLHCKCEPVPAEFYVIAAWLLWMLFWDVQIIAYVDGGCCEDHKVRVRLWGKDIKEPIKHYHPHCNPETNCHTHYYVLTLPAREFWKYRWVKFEYISPDGGKTQTAALWF | |
| >Pembrolizumab Heavy Chain | |
| QVQLVQSGVEVKKPGASVKVSCKASGYTFTNYYMYWVRQAPGQGLEWMGGINPSNGGTNFNEKFKNRVTLTTDSSTTTAYMELKSLQFDDTAVYYCARRDYRFDMGFDYWGQGTTVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRV | |
| >Pemfauxlizumab Heavy Chain | |
| EYKASCSRPIFCPIGETATITCTISGRDPRDENIMFYYRKPWGEMKYIGTVDTDDGKTTYDEEWKENVIATWDDDNNSATLTIKNLTRDMMMWFHVCVMDKKDGKGIDYCFSSARLFVFDKPFAAITAKKKDKAEIEVIACYPFHCHVSVGDGDDKDKLTQHYWKYTEDGYMICRVTKEKKVTAYCHRAGAKATIEE |
colbyford
/ CC12.3_B.1.1.529_HADDOCK_results_table.csv
Created
November 28, 2021 15:30
SARS-CoV-2 B.1.1.529 HADDOCK docking results with the CC12.3 antibody
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| Metric | 6XC7 RBD w/ CC12.3 | Predicted B.1.1.529 RBD w/ CC12.3 | % Difference | |
|---|---|---|---|---|
| Van der Waals energy | -86.1 | -93.1 | 8% | |
| Electrostatic energy | -248.1 | -194.1 | -22% | |
| Desolvation energy | -41.7 | -37.9 | -9% | |
| Restraints violation energy | 159.1 | 104.7 | -34% | |
| HADDOCK score | -161.5 | -159.4 | -1% | |
| Buried Surface Area | 2489.8 | 2416.7 | -3% |
colbyford
/ CC12.1_B.1.1.529_HADDOCK_results_table.csv
Created
November 28, 2021 15:14
SARS-CoV-2 B.1.1.529 HADDOCK docking results with the CC12.1 antibody
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| Metric | 6XC2 RBD w/ CC12.1 | Predicted B.1.1.529 RBD w/ CC12.1 | % Difference | |
|---|---|---|---|---|
| Van der Waals energy | -106.9 | -90.7 | -15% | |
| Electrostatic energy | -342.6 | -284.9 | -17% | |
| Desolvation energy | -37.5 | -28.8 | -23% | |
| Restraints violation energy | 143.2 | 152.6 | 7% | |
| HADDOCK score | -198.6 | -163.3 | -18% | |
| Buried Surface Area | 2778.5 | 2584.3 | -7% |
colbyford
/ spike_ref_vs_b11529.fasta
Created
November 26, 2021 19:43
Spike protein amino acid sequences between the SARS-CoV-2 NC 045512.2 reference genome and the B.1.1.529 variant
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| >NC_045512.2:21563-25384 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, SPIKE | |
| MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVR---DLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKL |
colbyford
/ SARS-CoV-2 B.1.1.529 Spike Mutations.md
Last active
November 29, 2021 16:03
SARS-CoV-2 B.1.1.529 Spike Mutations
| Type | Position | Ref | Alt | Ref Type | Alt Type | Type Difference |
|---|---|---|---|---|---|---|
| Substitution | 67 | A | V | Non-Polar | Non-Polar | No |
| Deletion | 69 | H | - | Positive | ||
| Deletion | 70 | V | - | Non-Polar | ||
| Substitution | 95 | T | I | Polar | Non-Polar | Yes |
| Substitution | 142 | G | D | Non-Polar | Negative | Yes |
| Deletion | 143 | V | - | Non-Polar | ||
| Deletion | 144 | Y | - | Polar | ||
| Deletion | 145 | Y | - | Polar |
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