Martínez Ríos, Félix Orlando

Main Affiliation

Official Name

ORCID

0000-0002-2346-5922

Preferred name

Martínez Ríos, Félix Orlando

Researcher ID

N-7502-2018

Scopus Author ID

24339038500

Now showing 1 - 10 of 43

Some of the metrics are blocked by your
consent settings
Half-Space Proximal Networks (HSPNs): A Proxy for Multi-Query Similarity Searching Models Predicting Tumor-Homing Peptides
(American Chemical Society (ACS), 2025-11-05)
Maylin Romero
;
;
;
Guillermin Agüero-Chapin
;
Longendri Aguilera-Mendoza
Some of the metrics are blocked by your
consent settings
In Silico Identification of Potential Clovibactin-like Antibiotics Binding to Unique Cell Wall Precursors in Diverse Gram-Positive Bacterial Strains
(MDPI, 2025-02-18)
Sierra-Hernandez, Olimpo
;
Saurith-Coronell, Oscar
;
Rodríguez-Macías, Juan
;
Márquez, Edgar
;
Ramón Mora, José
The rise in multidrug-resistant bacteria highlights the critical need for novel antibiotics. This study explores clovibactin-like compounds as potential therapeutic agents targeting lipid II, a crucial component in bacterial cell wall synthesis, using in silico techniques. A total of 2624 clovibactin analogs were sourced from the PubChem database and screened using ProTox 3.0 software based on their ADME-Tox properties, prioritizing candidates with favorable pharmacokinetic profiles and minimal toxicity. Molecular docking protocols were then employed to assess the binding interactions of the selected compounds with lipid II. Our analysis identified Compound 22 as a particularly promising candidate, exhibiting strong binding affinity, stable complex formation, and high selectivity for the target. Binding energy analysis, conducted via molecular dynamics simulations, revealed a highly negative value of −25.50 kcal/mol for Compound 22, surpassing that of clovibactin and underscoring its potential efficacy. In addition, Compound 22 was prioritized due to its exceptional binding affinity to lipid II and its favorable ADME-Tox properties, suggesting a lower likelihood of adverse effects. These characteristics position Compound 22 as a promising candidate for further pharmacological development. While our computational results are encouraging, experimental validation is essential to confirm the efficacy and safety of these compounds. This study not only advances our understanding of clovibactin analogs but also contributes to the ongoing efforts to combat antimicrobial resistance through innovative antibiotic development. ©The authors ©International Journal of Molecular Sciences ©MDPI.
Some of the metrics are blocked by your
consent settings
Mapping the Chemical Space of Antiviral Peptides with Half-Space Proximal and Metadata Networks Through Interactive Data Mining
(MDPI AG, 2025-10-03)
Daniela de Llano García
;
;
Guillermin Agüero-Chapin
;
Hortensia Rodríguez
;
Francesc J. Ferri
<jats:p>Antiviral peptides (AVPs) are promising therapeutic candidates, yet the rapid growth of sequence data and the field’s emphasis on predictors have left a gap: the lack of an integrated view linking peptide chemistry with biological context. Here, we map the AVP landscape through interactive data mining using Half-Space Proximal Networks (HSPNs) and Metadata Networks (MNs) in the StarPep toolbox. HSPNs minimize edges and avoid fixed thresholds, reducing computational cost while enabling high-resolution analysis. A threshold-free HSPN resolved eight chemically and biologically distinct communities, while MNs contextualized AVPs by source, function, and target, revealing structural–functional relationships. To capture diversity compactly, we applied centrality-guided scaffold extraction with redundancy removal (90–50% identity), producing four representative subsets suitable for modeling and similarity searches. Alignment-free motif discovery yielded 33 validated motifs, including 10 overlapping with reported AVP signatures and 23 apparently novel. Motifs displayed category-specific enrichment across antimicrobial classes, and sequences carrying multiple motifs (≥4–5) consistently showed higher predicted antiviral probabilities. Beyond computational insights, scaffolds provide representative “entry points” into AVP chemical space, while motifs serve as modular building blocks for rational design. Together, these resources provide an integrated framework that may inform AVP discovery and support scaffold- and motif-guided therapeutic design.</jats:p>
Some of the metrics are blocked by your
consent settings
Ligand-Based Virtual Screening Workflow for Antimalarial Repositioning from Known Drugs and Chemical Libraries
(Springer Nature Switzerland, 2025-10-11)
Machado-Tugores,Yanetsy
;
Meneses-Marcel, Alfredo
;
;
;
Cristina Aguilar, Ana
The present report outlines a workflow integrating various virtual screening methods to identify potential antimalarial compounds. To develop QSAR models, a dataset of 2,314 compounds was analyzed using linear discriminant analysis and the QuBiLs-MAS software. 37 individual models were generated and subsequently combined into a fusion-based multiclassifier system (MCS), which achieved predictive performances of 91.35% for the training set and 92.06% for the test set. The MCS was further evaluated through a virtual screening simulation involving 13,410 compounds from GlaxoSmithKline, yielding an extrapolation rate of 91.43%. Following this, several drug-likeness filters, the finalized MCS, and chemical diversity analyses were applied to select candidate compounds from three datasets for parasitological assays. Using the proposed in silico pipeline, a total of 6,811 drugs, 15,000 chemical compounds, and 1,120 biologically active molecules from the DrugBank, PrintScreen15, and Tocriscreen collections, respectively, were virtually screened. From these, 80 compounds were shortlisted as potential antimalarial candidates. Ultimately, 15 compounds were purchased and tested in vitro against two Plasmodium falciparum strains (3D7 and Dd2). Of these, five drugs (ziprasidone, isradipine, amcinonide, triflupromazine, and anisotropine) and four chemical compounds (NGB 2904, A23187, Otava-7019050991, and Otava-1677649) demonstrated antimalarial activity, with values μ. This approach represents a promising computational tool for the early stages of antimalarial drug discovery. ©The authors ©Springer.
Some of the metrics are blocked by your
consent settings
StarPepWeb: an integrative, graph-based resource for bioactive peptides
(Oxford University Press (OUP), 2024-12-26)
Christian López
;
Roberto Cárdenas
;
Longendri Aguilera-Mendoza
;
Guillermin Agüero-Chapin
;
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>The rapid growth of bioactive peptide sequences presents challenges for organization and analysis. Existing repositories often specialize in functions, taxonomic origins, or structural classes, but most remain isolated, use heterogeneous metadata, and lack uniform descriptors or structural models. Few integrative web services exist, offering only partial coverage or depth. As a result, reproducible and comprehensive exploration of the bioactive peptide landscape remains limited, underscoring the need for a unified, source-tracked, extensible platform.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>We present StarPepWeb, a freely accessible web application that democratizes access to StarPepDB, one of the largest curated repositories of bioactive peptides. The platform integrates 45 120 non-redundant sequences from 40 public databases into a source-tracked graph enriched with metadata, physicochemical features, and predicted 3D structures from ESMFold. Each peptide is represented with ESM-2 embeddings and iFeature descriptors, while the interface supports metadata-aware filtering, alignment-based similarity searches with single and multiple queries, and interactive visualization. A microservice-oriented architecture ensures scalability, maintainability, and reproducible versioned downloads, including Neo4j exports. StarPepWeb thus overcomes deployment and expertise barriers of the standalone database, providing an extensible, cloud-hosted framework for integrative bioactive peptide analysis.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>StarPepWeb is freely available at https://starpepweb.org. Source code and documentation are hosted at https://github.com/starpep-web.</jats:p> </jats:sec>
Some of the metrics are blocked by your
consent settings
A hybrid simulated annealing and threshold accepting for satisfiability problems using dynamically cooling schemes
(2007)
;
Frausto-Solís, Juan
For Satisfiability (SAT) Problem there is not a deterministic algorithm able to solve it in a polynomial time. Simulated Annealing (SA) and similar algorithms like Threshold Accepting (TA) are able to find very good solutions of SAT instances only if their control parameters are correctly tuned. Classical TA usually uses the same Markov chain length for each temperature cycle but they spend a lot of time. In this paper a method based on the neighborhood structure to get the Markov chain length in a dynamical way for each temperature cycle is proposed. Three cooling schemes are also presented in the paper. The experimentation presented in the paper shows that the proposed method is more efficient than the classical one.
46 1
Some of the metrics are blocked by your
consent settings
An efficient method to compare latencies in order to obtain the best route for SDN
(2017)
Elguea, Lorenzo M.
;
Comparing two or more routes on Internet is difficult owing to the variability of the measurements resulting from the different routes or use conditions. With current tools such as SDN[1], it is important to determine with certainty which the best route between a user and an internet service. This will be achieved with fast measurements which do not affect the operation of the network. With trends such as IoT, the best routes can be identified based on latency and not just on the jumps between autonomous systems, fact that optimizes data traffic in a specific way whether it is IPv4 or IPv6. As time elapses, it becomes more important to have a perfect setting for the LAN, which means optimal DNS, LDAP Servers appropriate number, etc. Thats why we propose a precise method that contemplates every possible variation of data, thus making a comparison by means of the use of confidence limits.
Scopus© Citations 6 11 1
Some of the metrics are blocked by your
consent settings
A new swarm algorithm for global optimization of multimodal functions over multi-threading architecture hybridized with simulating annealing
(2018)
;
Murillo-Suarez, Alfonso
This paper presents a new algorithm, PCLPSO, based on particle swarm optimization, which uses comprehensive learning particle swarm optimizer. Our algorithm executes C parallel CLPSO algorithms. We adopted as a criterion of completion a maximum value of evaluations of the objective function. During the execution of the CLPSO algorithms, when a certain evaluation value of the functions is reached, the best k are selected, and different initialization criteria are applied to continue the execution of the CLPSO algorithms: restarting the worst ones for the best solution or restores the worst ones to a random solution. For this restart, we use the Boltzmann criterion in a similar way as Simulating Annealing (SA) does. In this work, the experimental results obtained for the search of the minimum of 16 multimodal test functions such as Rosenbrock, Griewank, Rastrigin, Brannin, Schwefel, and others. Our algorithm proved to be more efficient than the traditional CLPSO in its experimental results, and the nonparametric Wilcoxon test confirmed this.
Scopus© Citations 7 18 1
Some of the metrics are blocked by your
consent settings
New Particle Swarm Optimizer Algorithm with Chaotic Maps for Combinatorial Global Optimization Problems. An Application to the Deconvolution of Mössbauer Spectra
(Springer, 2024-01-01)
;
;
González Morfín, Juan
In this chapter, we present a novel method for addressing global optimization problems inspired by evolutionary algorithms found in nature. We integrate the Comprehensive Learning Particle Swarm Optimization (CLPSO) algorithm with random value generation based on chaotic maps. The resulting algorithm is applied to the computationally complex task of deconvoluting Mossbauer spectra. We implement ten chaotic maps to generate random values and compare their performance with traditional random number generators. Through experiments, we demonstrate that the developed algorithm excels in exploring the search space and exhibits fast intensification in finding the global minimum. In addition, we perform a comprehensive review of existing solutions to the Mossbauer spectrum deconvolution problem, highlighting the scarce availability of developments in this area. We also present a user-friendly program designed with an intuitive interface to facilitate the deconvolution process by Spector Mossbauer. This program will be freely distributed without operational restrictions. Experimental validation is performed on Mossbauer spectra generated using the developed program and those obtained by experimental means, affirming the efficiency of the new algorithm conceived. ©Springer.
51
Some of the metrics are blocked by your
consent settings
Golden Ratio Annealing for Satisfiability Problems Using Dynamically Cooling Schemes
(2008)
Frausto-Solís, Juan
;
Abstract Satisfiability (SAT) Problem is an NP-Complete problem which means no deterministic algorithm is able to solve it in a polynomial time. Simulated Annealing (SA) can find very good solutions of SAT instances if its control parameters are correctly tuned. SA can be tuned experimentally or by using a Markov approach; the latter has been shown to be the most efficient one. Moreover Golden Ratio (GR) is an unconventional technique used to solve many problems. In this paper a new algorithm named Golden Ratio for Simulated Annealing (GRSA) is presented; it is tuned for three different cooling schemes. GRSA uses GR to dynamically decrease the SA temperature and a Markov Model to tune its parameters. Two SA tuned versions are compared in this paper: GRSA and a classical SA. Experimentation shows that the former is much more efficient than the latter. © Springer Nature
Scopus© Citations 3 34 2

Martínez Ríos, Félix Orlando

Filters

Settings

Sort By

Results per page