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Soft Computing Methods for Disulfide Connectivity Prediction

Alfonso E. Márquez-Chamorro, Jesús S. Aguilar-Ruiz
2015 Evolutionary Bioinformatics  
The problem of protein structure prediction (PSP) is one of the main challenges in structural bioinformatics. To tackle this problem, PSP can be divided into several subproblems. One of these subproblems is the prediction of disulfide bonds. The disulfide connectivity prediction problem consists in identifying which nonadjacent cysteines would be cross-linked from all possible candidates. Determining the disulfide bond connectivity between the cysteines of a protein is desirable as a previous
more » ... ep of the 3D PSP, as the protein conformational search space is highly reduced. The most representative soft computing approaches for the disulfide bonds connectivity prediction problem of the last decade are summarized in this paper. Certain aspects, such as the different methodologies based on soft computing approaches (artificial neural network or support vector machine) or features of the algorithms, are used for the classification of these methods.
doi:10.4137/ebo.s25349 pmid:26523116 pmcid:PMC4620934 fatcat:nucsnwhfnvb77bndwkjwmgpazi

Context-Aware Process Performance Indicator Prediction

Alfonso E. Marquez-Chamorro, Kate Revoredo, Manuel Resinas, Adela Del-Rio-Ortega, Flavia M. Santoro, Antonio Ruiz-Cortes
2020 IEEE Access  
Formally, we can express a 172 trace as an ordered list of events T i = [E i1 , . . . , E im ] where 173 E i1 represents the first event and E im the final event of trace 174 T i .  ...  for I from the trace [E i1 , . . . , E i l ], where E i1 is the first event and E i l is the last event that have occurred in trace T i at a given moment. data information of the traces.  ... 
doi:10.1109/access.2020.3044670 fatcat:nilvevmdc5dd5cjszu46yqogcq

Alpha Helix Prediction Based on Evolutionary Computation [chapter]

Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar Ruiz, Gualberto Asencio Cortés
2010 Lecture Notes in Computer Science  
Multiple approaches have been developed in order to predict the protein secondary structure. In this paper, we propose an approach to such a problem based on evolutionary computation. The proposed approach considers various amino acids properties in order to predict the secondary structure of a protein. In particular, we will consider the hydrophobicity, the polarity and the charge of amino acids. In this study, we focus on predicting a particular kind of secondary structure: α-helices. The
more » ... lts of our proposal will be a set of rules that will identify the beginning or an end of such a structure.
doi:10.1007/978-3-642-16001-1_31 fatcat:lcwqfklcvzgxdnhmvcg7zizt2e

Residue-Residue Contact Prediction Based on Evolutionary Computation [chapter]

Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar-Ruiz, Gualberto Asencio Cortés
2011 Advances in Intelligent and Soft Computing  
Two amino acids in a protein are in contact if the distance between them is less Alfonso Márquez Chamorro, Federico Divina, Jesús S.  ...  The list of PDB protein identifiers can be downloaded at http://www.upo.es/eps/marquez/ proteins.txt.  ... 
doi:10.1007/978-3-642-19914-1_37 dblp:conf/pacbb/ChamorroDAC11 fatcat:fu4zqt44knb5pogsfvqq6vp7mu

Improving the Efficiency of MECoMaP: A Protein Residue-Residue Contact Predictor [chapter]

Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar-Ruiz, Cosme E. Santiesteban Toca
2013 Lecture Notes in Computer Science  
This work proposes an improvement of the multi-objective evolutionary method for the protein residue-residue contact prediction called MECoMaP. This method bases its prediction on physicochemical properties of amino acids, structural features and evolutionary information of the proteins. The evolutionary algorithm produces a set of decision rules that identifies contacts between amino acids. These decision rules generated by the algorithm represent a set of conditions to predict residue-residue
more » ... contacts. A new encoding used, a fast evaluation of the examples from the training data set and a treatment of unbalanced classes of data were considered to improve the the efficiency of the algorithm.
doi:10.1007/978-3-642-41827-3_21 fatcat:gvrasfysdnaclcmhjyhunfass4

Prediction of Protein Distance Maps by Assembling Fragments According to Physicochemical Similarities [chapter]

Gualberto Asencio Cortés, Jesús S. Aguilar-Ruiz, Alfonso E. Márquez Chamorro
2011 Advances in Intelligent and Soft Computing  
The prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein consists of determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled according to their physicochemical similarities, using information extracted from known protein structures. Many approaches cited in the literature
more » ... se the physicochemical properties of amino acids, generally hydrophobicity, polarity and charge, to predict structure. In our method, implemented with parallel multithreading, a set of 30 physicochemical amino acid properties selected from the AAindex database were used. Several protein tertiary structure prediction methods produce a contact map. Our proposed method produces a distance map, which provides more information about the structure of a protein than a contact map. The results of experiments with several non-homologous protein sets demonstrate the generality of this method and its prediction quality using the amino acid properties considered.
doi:10.1007/978-3-642-19914-1_36 dblp:conf/pacbb/CortesAC11 fatcat:tdi6wsgppvhsnbi35h2s56rpla

Oscar Flores Flores (Coord.), El clasicismo en la época de Pedro José Márquez (1741-1820). Arqueología, filología, historia, música y teoría arquitectónica, México, Universidad Nacional Autónoma de México, Instituto de Investigaciones Estéticas / Real Aca

Antonio Astorgano Abajo
2016 Antiguos jesuitas en Iberoamérica  
son María del Carmen Rovira Gaspar ("Humanismo y pluriculturalismo en Pedro José Márquez", pp. 459-464); Alfonso Rodríguez y G. de Ceballos ("Pedro José Márquez en el contexto de la cultura humanística  ...  Arqueología histórica, México, Instituto Nacional de Antropología e Historia-Centro INAH Sinaloa, 2015, 210 pp. ISBN: 978-607-8039-58-6. D. Chamorro Espinosa, S.I, A. Astorgano Abajo, G.  ... 
doi:10.31057/2314.3908.v3.n2.17683 doaj:7782e0b60634400bb7554588b2982993 fatcat:sds627arr5ezjdn6cdegttcqum

Page 14 of Mathematical Reviews Vol. , Issue 2003A [page]

2003 Mathematical Reviews  
Marquez [Alberto Marquez] and A. Moreno-Gonzalez, Graphs with no dilation 00 GENERAL 14 (Spanish) (187-195); J. Caceres, F. Ledesma, A. Marquez [AI- berto Marquez] and A.  ...  Blanquero-Bravo] and E.  ... 

Arbitros revista Educación Química

2014 Educacion Quimica  
Luis Alfonso Torres, Departamento de Química, CINVESTAV, DF. 44. Ricardo Navarro Mendoza, Universi- dad de Guanajuato. Árbitros del extranjero 45.  ...  Ana Laura Márquez, Facultad de Medicina. 24. Ana María Sosa, Colegio de Ciencias y Humanidades, Plantel Sur. 25. Arcelia Ramírez, Escuela Nacional Preparatoria, Plantel 5. 26.  ... 
doi:10.1016/s0187-893x(14)70071-0 fatcat:mwbwu2aysrg65aqfdpvfbq5f24

Page 239 of World's Work Vol. 29, Issue 2 [page]

1914 World's Work  
-C., PERU Feperico ALFONSO PEZET, M., Elmer F. Mackusick, oe E. J. Louis, a ots Enrique Grau, Cc. Bruce Cartwright, Jr., ae C Hiram Slifer, } Carlos Ferreyros y Ayulo Cc. O. G. H. E.  ...  Guard Ci Augusto Marquez, H. ¢ Antonio Navarro E., OF Rodolso Perez, C..G.; Nathan Eisenmann, mV. James F. Ferguson, Vay, Arthur P. Cushing, Gs Burwell Richard, BCs Loren O.  ... 

Santo Toribio de Mogrovejo: de la extensión del culto a Patrono del Episcopado Latinoamericano

Mario L. Grignani
2013 Studium Veritatis  
H. en el Señor. + Fermín E.  ...  Manual litúrgico: Barcelona: E.  ... 
doi:10.35626/sv.17.2013.84 fatcat:vot23lhqm5gcfbrsuky6r54lna

Reviewers of Óptica Pura y Aplicada in the period 2006-2011

Ignacio Moreno, David Mas
2012 Óptica Pura y Aplicada  
Bilmes Centro de Investigaciones Ópticas, La Plata, Argentina Ralf Blendowske Darmstadt University of Applied Sciences, Alemania Alfonso Blesa Universidad de Zaragoza, España Salvador Bosch Universidad  ...  Universidad de Valladolid, España Jesús Marcen Universidad Complutense de Madrid, España Susana Marcos Instituto de Óptica, CSIC, Madrid, España Tomás Marqués University of Washington, USA Andrés Márquez  ... 
doi:10.7149/opa.45.1.i fatcat:5lpy4ugoknambf6poqhlnmy2oq

Analysis of scientific social networks participating in the: "XI National and IV International meeting of animal and veterinary sciences – ENICIP"¤

Mario F Cerón-Muñoz, Luis F Galeano, Ana M Mesa
2011 Revista Colombiana de Ciencias Pecuarias  
El objetivo del evento fue y continúa siendo la divulgación de trabajos de investigación a la comunidad académica del sector (Maldonado, 2004 y Márquez, 2009 ).  ...  El profesor Diego Chamorro (336) La temática de epidemiología se caracterizó por presentar varias redes (17) con una baja relación de investigadores dentro de una misma red (Figura 4).  ... 
doaj:db3ba36b16fb4a1e94e0be959af4b9fe fatcat:xrgzpdlmczci3c5eo4yjabt724

Colonialismo y santidad en las islas Marianas: los soldados de Gedeón (1676-1690)

Alexandre Coello de la Rosa
2010 Hispania  
RESUMEN: En este artículo analizo la conquista y conversión de las Marianas (1676de las Marianas ( -1690 como una realidad discursiva que transformó las islas en un teatro de violencia donde los chamorros  ...  Los hagiógrafos jesuitas elevaron a sus mártires a la categoría de «héroes» espirituales, transformando sus hazañas en un fuerte elemento de cohesión e identidad para los misioneros destinados en el archipiélago  ...  En las Siete Partidas de Alfonso X (1252-1284) este crimen se asociaba a quien atentaba contra la imagen o la vida de su rey, ya fuera asesinándolo, deponiéndolo o conspirando contra él.  ... 
doi:10.3989/hispania.2010.v70.i234.150 fatcat:rdehwyweojaitj7s6ha4kjr2tm

Índice de artículos publicados

John Harold Estrada Montoya
2017 Acta Odontológica Colombiana  
para mejorar la visibilidad en internet de una clínica odontológica (Free tools of e-marketing for web visibility in a dental clinic) Julián Alfonso Orjuela Benavides y John Harold Estrada Montoya  ...  Guitiérrez, Alfonso Delgado F. ACTA ODONTOLÓGICA COLOMBIANA. Volumen 3, número 2.  ... 
doaj:ef976115ba8a4cb8a4f4175941771806 fatcat:pnrvm7xkdbbkffy4ich5niwssq
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