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PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL.

Bramucci E, Paiardini A, Bossa F, Pascarella S - BMC Bioinformatics (2012)

Bottom Line: A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks.Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Scienze Biochimiche A, Rossi Fanelli, Sapienza Università di Roma, Roma 00185, Italy.

ABSTRACT

Background: In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.

Results: A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.

Conclusions: PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool.Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html.

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Secondary structure colouring method. The user can color the protein sequences by their secondary structure or by the physicochemical properties of their amino acids. The secondary structure assignment is based on the proSS algorithm http://roselab.jhu.edu/utils/pross.html.
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Figure 4: Secondary structure colouring method. The user can color the protein sequences by their secondary structure or by the physicochemical properties of their amino acids. The secondary structure assignment is based on the proSS algorithm http://roselab.jhu.edu/utils/pross.html.

Mentions: Once retrieved sequences from selected databases are loaded in PyMod, they can be used to generate a multiple sequence alignment by means of MUSCLE and ClustalW programs. The choice of two multiple sequence alignment tools is twofold: on the one hand, ClustalW is famous and very popular among people with limited experience in the field; on the other hand, MUSCLE is known to outperform ClustalW in quality and in speed. Future implementation of additional tools (e.g., T-Coffe [17]) is planned. Additionally, PyMod can input and output multiple alignments in the popular FASTA and Clustal formats. Different multiple alignments can be built for each cluster of sequences that is available in PyMod. The user from within an apposite PyMod window can control a number of ClustalW parameters. When dealing with sequence alignments comprising known 3D-structures, it is always more desirable to exploit this kind of information, by performing structural superposition and deriving a structure-based alignment. In this case, users can carry out a multiple structural alignment by using the combinatorial extension algorithm, implemented in the popular program CE, a fast and robust algorithm in superposing and aligning 3D-structures [11]. The selected 3D-structures are then automatically superposed in PyMOL, and the resulting structural alignment is displayed in PyMod. If the 3D-structures to be superposed and aligned have been previously aligned to their own sequence cluster with MUSCLE or ClustalW, users can optionally keep the latter, by using the structural alignment as guide to "merge" the two alignments. In this way, structure-based alignments are used as a template for realigning the original sequences, obtaining a structure-based multiple sequence alignment that combines sequences and structures. This procedure is similar to the one already implemented in the 3DCoffe tool [18]. The option to generate mixed structure-sequence alignment is particularly useful when two or more evolutionarily distant structural templates and their close orthologous sequences have to be aligned. In this scenario, the structural alignment of templates (which, being based on structure superposition, would outperform any sequence-based method) will provide the starting point for the subsequent merging of orthologous sequences, which have been previously aligned with MUSCLE or ClustalW. Most importantly, manually editing multiple sequence alignments in PyMod will allow the user to apply her/his knowledge to correct any misaligned residue. This option in PyMod simply requires the user to click with the mouse at the desired sequence position and then to drag residues to the right/left to add/remove gaps. The ability to edit sequences is another feature implemented in PyMod. Indeed, during modeling tasks, it is often necessary to mutate and/or trim existing sequences at their ends. This option, for example, helps to prevent long overhanging fragments after a MODELLER run. Excising part of the sequence in the middle is also possible. Finally, a number of coloring options for sequences are available via the PyMod menu, including a secondary structure scheme for sequences related to 3D-structures (Figure 4).


PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL.

Bramucci E, Paiardini A, Bossa F, Pascarella S - BMC Bioinformatics (2012)

Secondary structure colouring method. The user can color the protein sequences by their secondary structure or by the physicochemical properties of their amino acids. The secondary structure assignment is based on the proSS algorithm http://roselab.jhu.edu/utils/pross.html.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3303726&req=5

Figure 4: Secondary structure colouring method. The user can color the protein sequences by their secondary structure or by the physicochemical properties of their amino acids. The secondary structure assignment is based on the proSS algorithm http://roselab.jhu.edu/utils/pross.html.
Mentions: Once retrieved sequences from selected databases are loaded in PyMod, they can be used to generate a multiple sequence alignment by means of MUSCLE and ClustalW programs. The choice of two multiple sequence alignment tools is twofold: on the one hand, ClustalW is famous and very popular among people with limited experience in the field; on the other hand, MUSCLE is known to outperform ClustalW in quality and in speed. Future implementation of additional tools (e.g., T-Coffe [17]) is planned. Additionally, PyMod can input and output multiple alignments in the popular FASTA and Clustal formats. Different multiple alignments can be built for each cluster of sequences that is available in PyMod. The user from within an apposite PyMod window can control a number of ClustalW parameters. When dealing with sequence alignments comprising known 3D-structures, it is always more desirable to exploit this kind of information, by performing structural superposition and deriving a structure-based alignment. In this case, users can carry out a multiple structural alignment by using the combinatorial extension algorithm, implemented in the popular program CE, a fast and robust algorithm in superposing and aligning 3D-structures [11]. The selected 3D-structures are then automatically superposed in PyMOL, and the resulting structural alignment is displayed in PyMod. If the 3D-structures to be superposed and aligned have been previously aligned to their own sequence cluster with MUSCLE or ClustalW, users can optionally keep the latter, by using the structural alignment as guide to "merge" the two alignments. In this way, structure-based alignments are used as a template for realigning the original sequences, obtaining a structure-based multiple sequence alignment that combines sequences and structures. This procedure is similar to the one already implemented in the 3DCoffe tool [18]. The option to generate mixed structure-sequence alignment is particularly useful when two or more evolutionarily distant structural templates and their close orthologous sequences have to be aligned. In this scenario, the structural alignment of templates (which, being based on structure superposition, would outperform any sequence-based method) will provide the starting point for the subsequent merging of orthologous sequences, which have been previously aligned with MUSCLE or ClustalW. Most importantly, manually editing multiple sequence alignments in PyMod will allow the user to apply her/his knowledge to correct any misaligned residue. This option in PyMod simply requires the user to click with the mouse at the desired sequence position and then to drag residues to the right/left to add/remove gaps. The ability to edit sequences is another feature implemented in PyMod. Indeed, during modeling tasks, it is often necessary to mutate and/or trim existing sequences at their ends. This option, for example, helps to prevent long overhanging fragments after a MODELLER run. Excising part of the sequence in the middle is also possible. Finally, a number of coloring options for sequences are available via the PyMod menu, including a secondary structure scheme for sequences related to 3D-structures (Figure 4).

Bottom Line: A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks.Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Scienze Biochimiche A, Rossi Fanelli, Sapienza Università di Roma, Roma 00185, Italy.

ABSTRACT

Background: In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.

Results: A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.

Conclusions: PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool.Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html.

Show MeSH