julie-forman-kay-lab IDPConformerGenerator issues

julie-forman-kay-lab / IDPConformerGenerator

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space

https://idpconformergenerator.readthedocs.io/

Apache License 2.0

19 stars 6 forks source link

issues

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Implement residue substitution in the FASTA itself

#182 joaomcteixeira opened 2 years ago
2
Add instructions to install MCSCE

#181 joaomcteixeira closed 2 years ago
1
Mcsce implementation

#180 JerryJohnsonLee closed 2 years ago
3
Removes assert

#179 joaomcteixeira closed 2 years ago
0
improves regex dssp, adds validation

#178 joaomcteixeira closed 2 years ago
0
Update all documentation

#177 menoliu closed 2 years ago
1
Changed definitions of G to be included in H

#176 menoliu closed 2 years ago
0
corrects input command option

#175 joaomcteixeira closed 2 years ago
0
Add a tuned down parameter for ss propensity

#174 joaomcteixeira opened 2 years ago
0
Corrects csssconv definitions and groups "G" to "H

#173 menoliu closed 2 years ago
1
First attempt dropping the unnecessary first regex sampling

#172 joaomcteixeira closed 2 years ago
4
Documentation for the paper

#171 joaomcteixeira closed 2 years ago
10
Changes CSSS.JSON formatting to adopt new regex machinery

#170 menoliu closed 2 years ago
1
dropped tox-conda

#169 joaomcteixeira closed 2 years ago
0
Reviews the regex sampling machinery

#168 joaomcteixeira closed 2 years ago
5
Implemented other names in pdb files

#167 joaomcteixeira closed 2 years ago
0
Implements N-term Proline

#166 joaomcteixeira closed 2 years ago
1
Inconsistency in chunk size?

#165 joaomcteixeira closed 2 years ago
1
running without `-dr`

#164 joaomcteixeira closed 2 years ago
1
Ignore DSSP when sampling angles - sample only by residue type

#163 menoliu closed 2 years ago
3
corrects energy.log

#162 joaomcteixeira closed 2 years ago
0
Build can't find a solution after 600 conformers

#161 joaomcteixeira opened 2 years ago
0
Brings libfuncpy to the repository

#160 joaomcteixeira closed 2 years ago
0
[FEATURE] Custom Secondary Structure Sampling

#159 menoliu closed 2 years ago
12
new mmCIF assembly files

#158 joaomcteixeira opened 2 years ago
0
Updates to definitions to include DSSP-PPII "P" notation.

#157 menoliu closed 2 years ago
6
Update install and example

#156 joaomcteixeira closed 2 years ago
1
angle slice search based ONLY on residue nature, disregard DSSP info.

#155 joaomcteixeira closed 2 years ago
0
modify non-sidechain mask creation

#154 JerryJohnsonLee closed 3 years ago
3
update build_definitions

#153 JerryJohnsonLee closed 2 years ago
1
N-terminal for proline residues during topology creation

#152 joaomcteixeira closed 2 years ago
1
Implement toml based configuration file

#151 joaomcteixeira opened 3 years ago
0
Adpots MCSCE for packing sidechains

#150 joaomcteixeira closed 2 years ago
3
Sample pSer and pThr separately during backbone build

#149 joaomcteixeira opened 3 years ago
0
Add protons to PDB files using Gromacs

#148 SeanR22 opened 3 years ago
0
[DOCS] Add missing Hydrogens using ChimeraX and pdb-tools

#147 joaomcteixeira closed 3 years ago
0
Evaluate energy threshold for individual pairs - option

#146 joaomcteixeira closed 3 years ago
0
Add carbon alpha hydrogens regardless of the sidechain packing algorithm

#145 joaomcteixeira opened 3 years ago
0
Have the energy thresholds be defined by residue instead of the sum of residues.

#144 joaomcteixeira closed 3 years ago
0
Make folder bug

#143 joaomcteixeira closed 3 years ago
0
changed libfuncpy reference to .yml

#142 joaomcteixeira closed 3 years ago
0
Fully configurable peptide chunksize and probabilities

#141 joaomcteixeira closed 3 years ago
0
Effect of -etbb value on conformer generation rate

#140 SeanR22 opened 3 years ago
5
build now prints to terminal

#139 joaomcteixeira closed 3 years ago
0
The size of the chunks should be fully configurable

#138 joaomcteixeira closed 3 years ago
2
Scripts to generate SAXS curves and analyze the size and energy distributions of conformers

#137 SeanR22 opened 3 years ago
0
understanding the energy threshold (cutoff) values after 0.0.20

#136 SeanR22 opened 3 years ago
9
[FEATURE] Decoupled energy threshold parameters

#135 joaomcteixeira closed 3 years ago
0
Use different programs to calculate secondary structure

#134 joaomcteixeira opened 3 years ago
0
Effect of sequence length on conformer generation speed and energies

#133 SeanR22 opened 3 years ago
1

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