Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics
Analyzing the conformational dynamics of short peptides from molecular dynamics (MD) simulations remains challenging. The high dimensionality of torsional space and the periodic nature of dihedral angles complicate statistical analysis and dimensionality reduction. This work presents an integrated c...
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2026
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| Online dostop: | https://doi.org/10.1021/acs.jpca.5c07760 http://hdl.handle.net/20.500.14066/4799 |
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| _version_ | 1870612064727203840 |
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| author | Fleitas Albrizzi, Luis Fernando |
| author2 | Gayoso Domínguez, Osmar Gabriel Colbes Sanabria, José Domingo Di Lella, Santiago Schaerer Serra, Christian Emilio Cabarcas Álvarez Cruz, Amaury |
| author2_role | author author author author author |
| author_browse | Cabarcas Álvarez Cruz, Amaury Colbes Sanabria, José Domingo Di Lella, Santiago Fleitas Albrizzi, Luis Fernando Gayoso Domínguez, Osmar Gabriel Schaerer Serra, Christian Emilio |
| author_facet | Fleitas Albrizzi, Luis Fernando Gayoso Domínguez, Osmar Gabriel Colbes Sanabria, José Domingo Di Lella, Santiago Schaerer Serra, Christian Emilio Cabarcas Álvarez Cruz, Amaury |
| author_role | author |
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| bitstream.url.fl_str_mv | http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/1/Analyzing%20peptide%20torsional%20dynamics%20an%20angular-displacement%20PCA%20pipeline%20for%20short-horizon%20prediction%20from%20molecular%20dynamics.pdf http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/4/jp5c07760_si_001.pdf http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/2/license_rdf http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/3/license.txt http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/5/Analyzing%20peptide%20torsional%20dynamics.jpg |
| dc.creator.none.fl_str_mv | Fleitas Albrizzi, Luis Fernando Gayoso Domínguez, Osmar Gabriel Colbes Sanabria, José Domingo Di Lella, Santiago Schaerer Serra, Christian Emilio Cabarcas Álvarez Cruz, Amaury |
| dc.date.accessioned.none.fl_str_mv | 2026-07-07T19:50:08Z |
| dc.date.available.none.fl_str_mv | 2026-07-07T19:50:08Z |
| dc.date.issued.none.fl_str_mv | 2026-04-22 |
| dc.identifier.citation.en.fl_str_mv | Corresponding Author. Amaury C. Alvarez − Institute of Computing, Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil; orcid.org/0000-0002-5513-7974; Email: amaury@ic.ufrj.br. Albrizzi, L., Gayoso, G., Colbes, J., Di Lella, S., Schaerer, C. E., & Alvarez, A. C. (2026). Analyzing Peptide Torsional Dynamics: An Angular-Displacement PCA Pipeline for Short-Horizon Prediction from Molecular Dynamics. The Journal of Physical Chemistry A, 130(18), 3665–3679. https://doi.org/10.1021/acs.jpca.5c07760 |
| dc.identifier.doi.es.fl_str_mv | 10.1021/acs.jpca.5c07760 |
| dc.identifier.essn.es.fl_str_mv | 1520-5215 |
| dc.identifier.issn.es.fl_str_mv | 1089-5639 |
| dc.identifier.other.es.fl_str_mv | https://doi.org/10.1021/acs.jpca.5c07760 |
| dc.identifier.uri.none.fl_str_mv | http://hdl.handle.net/20.500.14066/4799 |
| dc.language.iso.es.fl_str_mv | eng |
| dc.publisher.es.fl_str_mv | ACS Publications |
| dc.relation.institBenef.es.fl_str_mv | Universidad Nacional de Asunción. Facultad Politécnica |
| dc.relation.projectCONACYT.es.fl_str_mv | PINV01-277 ESTR01-23 BINV04-101 |
| dc.rights.*.fl_str_mv | Atribución/Reconocimiento 4.0 Internacional |
| dc.rights.accessRights.es.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.rights.copyright.es.fl_str_mv | © 2026 The Authors. Published by American Chemical Society |
| dc.rights.uri.*.fl_str_mv | http://creativecommons.org/licenses/by/4.0/ |
| dc.subject.classification.es.fl_str_mv | 13. Avance general del conocimiento: I+D financiada con fuentes distintas a los FGU 13.1. I+D relativa a las Ciencias Naturales |
| dc.subject.ocde.es.fl_str_mv | 1. Ciencias Naturales 1.2. Ciencias físicas (astronomía y ciencias del espacio, física, otras áreas afines) 2. Ingeniería y Tecnología 2.5. Ingeniería de los Materiales |
| dc.subject.other.es.fl_str_mv | Chemical structure Computational chemistry Mathematical methods Molecular dynamics Peptides and proteins |
| dc.title.es.fl_str_mv | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| dc.type.es.fl_str_mv | info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | Analyzing the conformational dynamics of short peptides from molecular dynamics (MD) simulations remains challenging. The high dimensionality of torsional space and the periodic nature of dihedral angles complicate statistical analysis and dimensionality reduction. This work presents an integrated computational workflow that combines all-atom MD simulations with a multistage analytical framework to characterize torsional reorganization patterns. Our approach introduces an angular-displacement representation χ that resolves periodic discontinuities by focusing on frame-to-frame torsional changes rather than absolute configurations. This transformation yields variables suitable for linear analysis and acts as a high-pass filter, emphasizing rapid reorganization events over slow conformational drift. We analyze these transformed coordinates using spatiotemporal principal component analysis (PCA) to identify collective torsional patterns. To evaluate how different coordinate choices preserve dynamical information, we quantitatively compare raw dihedral angles, sine–cosine embedding, and the displacement representation χ using the VAMP score. This comparison reveals their complementary nature: sine–cosine coordinates capture slow conformational variability, while χ highlights rapid torsional reorganizations. Subspace convergence analysis confirms the stability of the reduced PCA representation within the simulation time scale. We apply the methodology to the DENV-2 peptide (CGYGLC) as a representative short system. Our approach identifies hierarchical patterns of torsional flexibility─characterized by a flexible central core and region-specific dynamics─and reconstructs short-term structural evolution with angular errors below 25% and RMSD values of 1.0–2.1 Å. The main contributions are (i) a geometry-aware angular-displacement representation that respects the periodic nature of torsional variables; (ii) a spectral characterization of the displacement transformation; (iii) a quantitative comparison of observable representations using the VAMP score; and (iv) a demonstration of short-horizon structural prediction from reduced dynamical subspaces. The workflow provides a computationally efficient framework for analyzing torsional reorganization dynamics in peptide simulations. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | CONACYT_09f3c043dda320f3596a40bf3e51997c |
| identifier_str_mv | Corresponding Author. Amaury C. Alvarez − Institute of Computing, Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil; orcid.org/0000-0002-5513-7974; Email: amaury@ic.ufrj.br. Albrizzi, L., Gayoso, G., Colbes, J., Di Lella, S., Schaerer, C. E., & Alvarez, A. C. (2026). Analyzing Peptide Torsional Dynamics: An Angular-Displacement PCA Pipeline for Short-Horizon Prediction from Molecular Dynamics. The Journal of Physical Chemistry A, 130(18), 3665–3679. https://doi.org/10.1021/acs.jpca.5c07760 1089-5639 10.1021/acs.jpca.5c07760 1520-5215 |
| language | eng |
| network_acronym_str | CONACYT |
| network_name_str | Repositorio Institucional CONACYT |
| oai_identifier_str | oai:repositorio.conacyt.gov.py:20.500.14066/4799 |
| publishDate | 2026 |
| publishDateSort | 2026 |
| repository.mail.fl_str_mv | repositorio.institucional@conacyt.gov.py |
| repository.name.fl_str_mv | Repositorio Institucional CONACYT |
| repository_id_str | |
| rights_invalid_str_mv | Atribución/Reconocimiento 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ © 2026 The Authors. Published by American Chemical Society |
| spelling | 59cffb0f-e3cc-42cb-97cf-29432779d3eb60048294ff9-2ac8-4a35-9c21-44b7c4eb8e7a6002976000000-0002-7231-7563cd1d27dc-9819-471a-999f-52a8269bd3e36001062600b22bbc6f-317e-4998-adc4-cf4c4e73ce5c6002026-07-07T19:50:08Z2026-07-07T19:50:08Z2026-04-22Corresponding Author. Amaury C. Alvarez − Institute of Computing, Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil; orcid.org/0000-0002-5513-7974; Email: amaury@ic.ufrj.br.Albrizzi, L., Gayoso, G., Colbes, J., Di Lella, S., Schaerer, C. E., & Alvarez, A. C. (2026). Analyzing Peptide Torsional Dynamics: An Angular-Displacement PCA Pipeline for Short-Horizon Prediction from Molecular Dynamics. The Journal of Physical Chemistry A, 130(18), 3665–3679. https://doi.org/10.1021/acs.jpca.5c077601089-5639https://doi.org/10.1021/acs.jpca.5c07760http://hdl.handle.net/20.500.14066/479910.1021/acs.jpca.5c077601520-5215Analyzing the conformational dynamics of short peptides from molecular dynamics (MD) simulations remains challenging. The high dimensionality of torsional space and the periodic nature of dihedral angles complicate statistical analysis and dimensionality reduction. This work presents an integrated computational workflow that combines all-atom MD simulations with a multistage analytical framework to characterize torsional reorganization patterns. Our approach introduces an angular-displacement representation χ that resolves periodic discontinuities by focusing on frame-to-frame torsional changes rather than absolute configurations. This transformation yields variables suitable for linear analysis and acts as a high-pass filter, emphasizing rapid reorganization events over slow conformational drift. We analyze these transformed coordinates using spatiotemporal principal component analysis (PCA) to identify collective torsional patterns. To evaluate how different coordinate choices preserve dynamical information, we quantitatively compare raw dihedral angles, sine–cosine embedding, and the displacement representation χ using the VAMP score. This comparison reveals their complementary nature: sine–cosine coordinates capture slow conformational variability, while χ highlights rapid torsional reorganizations. Subspace convergence analysis confirms the stability of the reduced PCA representation within the simulation time scale. We apply the methodology to the DENV-2 peptide (CGYGLC) as a representative short system. Our approach identifies hierarchical patterns of torsional flexibility─characterized by a flexible central core and region-specific dynamics─and reconstructs short-term structural evolution with angular errors below 25% and RMSD values of 1.0–2.1 Å. The main contributions are (i) a geometry-aware angular-displacement representation that respects the periodic nature of torsional variables; (ii) a spectral characterization of the displacement transformation; (iii) a quantitative comparison of observable representations using the VAMP score; and (iv) a demonstration of short-horizon structural prediction from reduced dynamical subspaces. The workflow provides a computationally efficient framework for analyzing torsional reorganization dynamics in peptide simulations.Consejo Nacional de Ciencia y TecnologíaPrograma Paraguayo para el Desarrollo de la Ciencia y Tecnología. Proyectos de investigación y desarrolloPrograma Paraguayo para el Desarrollo de la Ciencia y Tecnología. Proyectos estratégicosPrograma Paraguayo para el Desarrollo de la Ciencia y Tecnología. Financiamiento de estancias de investigaciónengACS PublicationsAtribución/Reconocimiento 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccess© 2026 The Authors. Published by American Chemical Society13. Avance general del conocimiento: I+D financiada con fuentes distintas a los FGU13.1. I+D relativa a las Ciencias NaturalesChemical structureComputational chemistryMathematical methodsMolecular dynamicsPeptides and proteins1. Ciencias Naturales1.2. Ciencias físicas (astronomía y ciencias del espacio, física, otras áreas afines)2. Ingeniería y Tecnología2.5. Ingeniería de los MaterialesAnalyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamicsinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion18The Journal of Physical Chemistry A36653679PINV01-277ESTR01-23BINV04-101Universidad Nacional de Asunción. Facultad Politécnica130Fleitas Albrizzi, Luis FernandoGayoso Domínguez, Osmar GabrielColbes Sanabria, José DomingoDi Lella, SantiagoSchaerer Serra, Christian EmilioCabarcas Álvarez Cruz, AmauryORIGINALAnalyzing peptide torsional dynamics an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics.pdfAnalyzing peptide torsional dynamics an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics.pdfArtículo científicoapplication/pdf6760611http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/1/Analyzing%20peptide%20torsional%20dynamics%20an%20angular-displacement%20PCA%20pipeline%20for%20short-horizon%20prediction%20from%20molecular%20dynamics.pdfb20c647b642c1261d24cf705f0db3d69MD51jp5c07760_si_001.pdfjp5c07760_si_001.pdfInformación complementariaapplication/pdf393473http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/4/jp5c07760_si_001.pdf49df5c62a198b9016f402b9072c80419MD54CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8908http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/2/license_rdf0175ea4a2d4caec4bbcc37e300941108MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-81698http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/3/license.txt858b22fda432bd774e469302988c1974MD53THUMBNAILAnalyzing peptide torsional dynamics.jpgAnalyzing peptide torsional dynamics.jpgArtículo científicoimage/jpeg558686http://repositorio.conacyt.gov.py/bitstream/20.500.14066/4799/5/Analyzing%20peptide%20torsional%20dynamics.jpg668a548c9fbcd210c4393d2ce3e03758MD5520.500.14066/4799oai:repositorio.conacyt.gov.py:20.500.14066/47992026-07-07 20:23:52.946Repositorio Institucional CONACYTrepositorio.institucional@conacyt.gov.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 |
| spellingShingle | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics Fleitas Albrizzi, Luis Fernando 13. Avance general del conocimiento: I+D financiada con fuentes distintas a los FGU 13.1. I+D relativa a las Ciencias Naturales Chemical structure Computational chemistry Mathematical methods Molecular dynamics Peptides and proteins 1. Ciencias Naturales 1.2. Ciencias físicas (astronomía y ciencias del espacio, física, otras áreas afines) 2. Ingeniería y Tecnología 2.5. Ingeniería de los Materiales |
| status_str | publishedVersion |
| title | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| title_full | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| title_fullStr | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| title_full_unstemmed | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| title_short | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| title_sort | Analyzing peptide torsional dynamics : an angular-displacement PCA pipeline for short-horizon prediction from molecular dynamics |
| topic | 13. Avance general del conocimiento: I+D financiada con fuentes distintas a los FGU 13.1. I+D relativa a las Ciencias Naturales Chemical structure Computational chemistry Mathematical methods Molecular dynamics Peptides and proteins 1. Ciencias Naturales 1.2. Ciencias físicas (astronomía y ciencias del espacio, física, otras áreas afines) 2. Ingeniería y Tecnología 2.5. Ingeniería de los Materiales |
| url | https://doi.org/10.1021/acs.jpca.5c07760 http://hdl.handle.net/20.500.14066/4799 |