IDPConformerGenerator¶
IDPConformerGenerator is a flexible, modular platform for generating ensembles of disordered protein states that builds conformers by sampling backbone torsion angles of relevant sequence fragments extracted from protein structures in the RCSB Protein Data Bank.
IDPConformerGenerator can efficiently build large and diverse conformer pools of disordered proteins, with user defined options enabling variable fractional population of secondary structures, including matching those assigned based on NMR chemical shift data. These conformer pools are intended to be utilized as input for further approaches to match experimental data, such as re-weighting or sub-setting algorithms.
Note to users: IDR conformers generated with ldrs
, specifically processed
using the align_coords()
function in ldrs_helper.py
prior to v0.7.17
may have the wrong stereochemistry. This bug has since been fixed. Thank you for
your understanding and we apologize for any inconvenience this has caused.
Contents¶
- Installation
- Usage
- Command-lines
- IDPConfGen Small Peptide Example
- Building With Variable Bond-Geometry Strategies
- A Real Case Scenario
- Modeling Disordered Region Tails on a Folded Domain
- Modeling Disordered Regions Within Folded Domains
- Advanced LDRS Usage
- Processing Low-Confidence Predicted Residues
- Modeling Disordered Regions in a Multi-Chain Protein Complex
- Exploring IDPConfGen Analysis Functions
- Exploring MC-SCE and Int2Cart Integrations
- How to Efficiently Set Jobs up for HPC Clusters
- Using IDPConfgen as Python library
- F.A.Q.s
- What are the recommended hardware specifications?
- How long does the database generation take?
- What are the best options for combination of conformers and cores to use?
- What’s the difference between MC-SCE and FASPR?
- How can I optimize the MC-SCE settings for large proteins?
- What does it mean that IDPConformerGenerator is deterministic?
- What forcefield does IDPConformerGenerator use by default to generate PDB files?
- Out-of-memory (OOM) error when running the
count_clashes
function
- Reference
- Contributing
- How to cite
- Authors
- Versioning
- Changelog
- v0.7.23 (2024-03-27)
- v0.7.22 (2024-03-22)
- v0.7.21 (2024-03-13)
- v0.7.20 (2024-02-01)
- v0.7.19 (2024-01-29)
- v0.7.18 (2024-01-25)
- v0.7.17 (2024-01-20)
- v0.7.16 (2024-01-11)
- v0.7.15 (2024-01-05)
- v0.7.14 (2024-01-04)
- v0.7.13 (2024-01-03)
- v0.7.12 (2023-11-17)
- v0.7.11 (2023-11-02)
- v0.7.10 (2023-10-27)
- v0.7.9 (2023-10-27)
- v0.7.8 (2023-10-02)
- v0.7.7 (2023-09-26)
- v0.7.6 (2023-09-25)
- v0.7.5 (2023-09-11)
- v0.7.4 (2023-09-11)
- v0.7.3 (2023-09-11)
- v0.7.2 (2023-07-27)
- v0.7.1 (2023-07-27)
- v0.7.0 (2023-07-25)
- v0.6.17 (2023-06-12)
- v0.6.16 (2022-11-08)
- v0.6.15 (2022-09-26)
- v0.6.14 (2022-07-13)
- v0.6.13 (2022-07-13)
- v0.6.12 (2022-07-07)
- v0.6.11 (2022-06-14)
- v0.6.10 (2022-06-14)
- v0.6.9 (2022-06-13)
- v0.6.8 (2022-06-13)
- v0.6.7 (2022-05-31)
- v0.6.6 (2022-05-27)
- v0.6.5 (2022-05-25)
- v0.6.4 (2022-05-25)
- v0.6.3 (2022-05-25)
- v0.6.2 (2022-05-25)
- v0.6.1 (2022-05-25)
- v0.6.0 (2022-05-24)
- v0.5.1 (2022-05-24)
- v0.5.0 (2022-05-24)
- v0.4.10 (2022-05-23)
- v0.4.9 (2022-05-23)
- v0.4.8 (2022-05-23)
- v0.4.7 (2022-05-23)
- v0.4.6 (2022-04-22)
- v0.4.5 (2022-04-21)
- v0.4.4 (2022-03-29)
- v0.4.3 (2022-03-26)
- v0.4.2 (2022-03-20)
- v0.4.1 (2022-03-17)
- v0.4.0 (2022-03-15)
- v0.3.3 (2022-03-14)
- v0.3.2 (2022-03-14)
- v0.3.1 (2022-03-13)
- v0.3.0 (2022-03-13)
- v0.2.6 (2022-03-13)
- v0.2.5 (2022-03-11)
- v0.2.4 (2022-03-11)
- v0.2.3 (2022-03-08)
- v0.2.2 (2022-03-07)
- v0.2.1 (2022-03-03)
- v0.2.0 (2022-02-10)
- v0.1.0 (2021-07-24)
- v0.0.24 (2021-07-01)
- v0.0.23 (2021-07-01)
- v0.0.22 (2021-06-30)
- v0.0.21 (2021-06-28)
- v0.0.20 (2021-06-21)
- v0.0.19 (2021-06-14)
- v0.0.18 (2021-06-10)
- v0.0.17 (2021-06-10)
- v0.0.16 (2021-06-09)
- v0.0.15 (2021-06-09)
- v0.0.14 (2021-06-05)
- v0.0.13 (2021-05-28)
- v0.0.12 (2021-05-28)
- v0.0.11 (2021-05-28)
- v0.0.10 (2021-05-27)
- v0.0.9 (2021-05-27)
- v0.0.8 (2021-05-09)
- v0.0.7 (2021-05-09)
- v0.0.6 (2021-04-20)
- v0.0.5 (2021-04-19)
- v0.0.4 (2021-04-19)
- v0.0.3 (2021-04-19)
- v0.0.2 (2021-04-03)
- v0.0.1 (2021-04-02)
- v0.0.0