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smsaladi / matras_alpha.txt
Created June 30, 2019 16:41
Matras for IMP Symmetry
#### MATRAS VER 1.2: PROGRAM FOR PROTEIN 3D STRUCTURE COMPARISON ####
# coded by Takeshi Kawabata. Last Modified : 2017/09/15
#<REFERENCE>
# Takeshi Kawabata and Ken Nishikawa.
# "Protein Structure Comparison Using the Markov Transition Model of Evolution".
# Proteins vol.41:108-122(2000).
#<COMMAND> "Matras P -A 1bcc_sb.pdb -Ac C -B 1bcc_sb.pdb -Bc C -SA T "
#<DATE> "Jun 30,2019 9:27:4"
#<MODE> P:PAIRWISE COMPARISON
#<PARAMETERS>
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smsaladi / prep_hhsuite_cdd.sh
Created April 13, 2019 19:31
Prepare domain databases for HH-suite
#!/bin/bash
# prep for NCBI CDD
# Version is in `cdd.info`
# wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.info
# 3.17 at the time of writing
# mkdir cdd
# wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/fasta.tar.gz
@smsaladi
smsaladi / 10.1038_nbt4261_supplementary_sequences.fasta
Created October 11, 2018 21:32
Supplementary Sequences from Zong, et al., Nat. Biotechnol., 2018, doi:10.1038/nbt.4261
>A3A-PBE
ATGGAGGCCAGCCCGGCTAGCGGCCCAAGGCATCTCATGGACCCGCACATCTTCACCAGCAACTT
CAACAACGGCATCGGCAGGCACAAGACCTACTTGTGCTACGAGGTGGAGAGGCTCGACAACGGAA
CCTCCGTGAAGATGGACCAACACAGGGGGTTCCTCCACAACCAAGCCAAGAACCTCCTCTGCGGC
TTCTACGGCAGGCACGCCGAGTTGAGGTTCCTCGACTTGGTGCCATCCCTCCAACTCGATCCAGC
CCAAATCTACCGCGTGACCTGGTTCATCTCCTGGTCCCCATGCTTCTCCTGGGGTTGCGCCGGCG
AGGTTCGGGCTTTCCTCCAAGAAAACACCCACGTCCGCCTCCGCATTTTCGCCGCCAGGATCTAT
GATTACGACCCTCTCTACAAGGAGGCCCTCCAGATGCTGCGGGACGCCGGTGCTCAGGTGAGTAT
CATGACCTACGACGAGTTCAAGCACTGCTGGGACACCTTCGTTGACCACCAGGGCTGCCCATTCC
AACCATGGGACGGTCTGGATGAACACAGCCAAGCCTTGTCCGGCAGGCTCCGGGCCATCCTCCAA
@smsaladi
smsaladi / rsync_with_lock.sh
Last active February 1, 2018 19:42
#!/bin/bash
# A simple wrapper script to avoid starting an rsync process
# if one is currently running
#
# Shyam Saladi (saladi@caltech.edu)
#
# parts from
# https://superuser.com/a/848123/470760
#
@smsaladi
smsaladi / blockstack.txt
Created December 9, 2017 22:18
Verifying my Blockstack ID is secured with the address 1GvEXjctkhQMzwtp6NDrykwisikn381gp9 https://explorer.blockstack.org/address/1GvEXjctkhQMzwtp6NDrykwisikn381gp9
@smsaladi
smsaladi / keybase.md
Created December 9, 2017 21:39

Keybase proof

I hereby claim:

  • I am smsaladi on github.
  • I am saladi (https://keybase.io/saladi) on keybase.
  • I have a public key whose fingerprint is 0669 1F19 4CEA C84C 7516 E63B 5F7A DB2B AA5C E260

To claim this, I am signing this object:

@smsaladi
smsaladi / hydrophobic_moment.py
Created November 15, 2017 23:45 — forked from JoaoRodrigues/hydrophobic_moment.md
Peptide/Protein Hydrophobic Moment Calculator
#!/usr/bin/env python
"""
Calculates a set of properties from a protein sequence:
- hydrophobicity (according to a particular scale)
- mean hydrophobic dipole moment assuming it is an alpha-helix.
- total charge (at pH 7.4)
- amino acid composition
- discimination factor according to Rob Keller (IJMS, 2011)