CYLIB - Revision history

GuentertWiki at 17:52, 24 January 2026

2026-01-24T17:52:09Z

← Older revision		Revision as of 17:52, 24 January 2026
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	The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atsoms with fixed relative positions.		The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atsoms with fixed relative positions.

	~~The input topology-file must be either in MOL2 format (with extension .mol2) or in the mmCIF format of the PDB Chemical Component Dictionary (with extension .cif).~~

	== Availability ==		== Availability ==

GuentertWiki at 17:31, 24 January 2026

2026-01-24T17:31:58Z

← Older revision		Revision as of 17:31, 24 January 2026
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	CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from molecular topology descriptions given as [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] or [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] mmCIF files.		CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from molecular topology descriptions given as [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] or [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] mmCIF files.

	Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of molecules but ~~the process~~ is time-consuming and error-prone. CYLIB automates this process.		Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of molecules but is time-consuming and error-prone. CYLIB automates this process.

	The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atsoms with fixed relative positions.		The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atsoms with fixed relative positions.
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	== Availability ==		== Availability ==

	* CYLIB is [[CYLIB 2.2 Software License\|available]] free-of-charge. The current version is CYLIB 2.2.		* CYLIB is [[CYLIB 2.2 Software License\|available]] free-of-charge. The current version is CYLIB 2.2.

	== ~~References~~ ==		== Reference ==

	* Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary[https://uni-frankfurt.guentert.science/Reprints/Maden15-Cylib.pdf .] [http://doi.org/10.1007/s10858-015-9959-y J. Biomol. NMR 63, 21-37 (2015)]		* Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary[https://uni-frankfurt.guentert.science/Reprints/Maden15-Cylib.pdf .] [http://doi.org/10.1007/s10858-015-9959-y J. Biomol. NMR 63, 21-37 (2015)]

	:''Reports or publications of results obtained with CYLIB should cite this paper.''		:''Reports or publications of results obtained with CYLIB should cite this paper.''

GuentertWiki at 17:29, 24 January 2026

2026-01-24T17:29:28Z

@@ Line 4: / Line 4: @@
 CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from molecular topology descriptions given as [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] or [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] mmCIF files.
-CYLIB is an algorithm for converting molecular topology descriptions in MOL2 format or from the PDB
+Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of molecules but the process is time-consuming and error-prone. CYLIB automates this process.
-Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the
+The tree structure of torsion angles is needed by the CYANA structure calculation algorithm because it uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atsoms with fixed relative positions.
 == Availability ==

GuentertWiki at 17:24, 24 January 2026

2026-01-24T17:24:28Z

← Older revision		Revision as of 17:24, 24 January 2026
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	CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from ~~mmCIF files of the~~ [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or ~~[https://aideepmed~~.~~com/DockRMSD/~~mol2.~~pdf Tripos Mol2] files~~.		CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from molecular topology descriptions given as [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] or [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] mmCIF files.

			CYLIB is an algorithm for converting molecular topology descriptions in MOL2 format or from the PDB
			Chemical Component Dictionary into CYANA residue library entries.

			Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the
			process is time-consuming and error-prone. An automated method is necessary in order to handle the
			large number of different potential ligand molecules to be studied in drug design projects. CyLib is
			an algorithm for this purpose.
			The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient
			computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have
			to be represented in torsion angle space with rotations around covalent single bonds as the only
			degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid
			units composed of one or several atsoms with fixed relative positions. Setting up CYANA residue
			library entries therefore involves, besides straightforward format conversion, the non-trivial step
			of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is
			compatible with this tree structure. This can be done manually for small numbers of ligands but the
			process is time-consuming and error-prone. An automated method is necessary in order to handle the
			large number of different potential ligand molecules to be studied in drug design projects. CyLib is
			an algorithm for this purpose.

			The input topology-file must be either in MOL2 format (with extension .mol2) or in the mmCIF format
			of the PDB Chemical Component Dictionary (with extension .cif).


	With CYLIB you can easily:		With CYLIB you can easily:

GuentertWiki at 17:19, 24 January 2026

2026-01-24T17:19:42Z

← Older revision		Revision as of 17:19, 24 January 2026
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	''CYANA library ~~residue entry~~ preparation''		''CYANA library preparation''

GuentertWiki at 17:19, 24 January 2026

2026-01-24T17:19:02Z

← Older revision		Revision as of 17:19, 24 January 2026
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	* CYLIB is [[CYLIB 2.2 Software License\|available]] free-of-charge. The current version is CYLIB 2.2.		* CYLIB is [[CYLIB 2.2 Software License\|available]] free-of-charge. The current version is CYLIB 2.2.

	== ~~Documentation~~ ==		== References ==

	* [[~~Media~~:~~CofimaManual~~.~~pdf\|Manual~~ (~~PDF~~)]]		* Maden Yilmaz, E. & Güntert, P. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary[https://uni-frankfurt.guentert.science/Reprints/Maden15-Cylib.pdf .] [http://doi.org/10.1007/s10858-015-9959-y J. Biomol. NMR 63, 21-37 (2015)]

			:''Reports or publications of results obtained with CYLIB should cite this paper.''

GuentertWiki at 17:17, 24 January 2026

2026-01-24T17:17:00Z

← Older revision		Revision as of 17:17, 24 January 2026
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	CYLIB (© by Peter Güntert) can be used to prepare new entries for the CYANA residue library starting from mmCIF files ~~from~~ the [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] files.		CYLIB (© by Peter Güntert) can be used to prepare new entries for the [https://cyana.org/wiki/Residue_library_file CYANA residue library] starting from mmCIF files of the [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] files.

	With ~~COFIMA~~ you can easily:		With CYLIB you can easily:

	* Convert between different data file formats		* Convert between different data file formats

GuentertWiki: Created page with "''CYANA library residue entry preparation'' CYLIB (© by Peter Güntert) can be used to prepare new entries for the CYANA residue library starting from mmCIF files from the [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] files. With COFIMA you can easily: * Convert between different data file formats == Availability == * CYLIB is available free-of-charge...."

2026-01-24T17:15:22Z

Created page with "''CYANA library residue entry preparation'' CYLIB (© by Peter Güntert) can be used to prepare new entries for the CYANA residue library starting from mmCIF files from the [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] files. With COFIMA you can easily: * Convert between different data file formats == Availability == * CYLIB is available free-of-charge...."

New page

''CYANA library residue entry preparation''

CYLIB (© by Peter Güntert) can be used to prepare new entries for the CYANA residue library starting from mmCIF files from the [https://www.wwpdb.org/data/ccd PDB Chemical Component Dictionary] or [https://aideepmed.com/DockRMSD/mol2.pdf Tripos Mol2] files.

With COFIMA you can easily:

* Convert between different data file formats

== Availability ==
* CYLIB is [[CYLIB 2.2 Software License|available]] free-of-charge. The current version is CYLIB 2.2.

== Documentation ==

* [[Media:CofimaManual.pdf|Manual (PDF)]]