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ORCIDAndrzej Kloczkowski
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Journal Articles
- 2022
[j18]Enrique J. deAndrés-Galiana
, Juan Luis Fernández Martínez, Óscar Álvarez-Machancoses, Guillermina Bea, Carlos M. Galmarini, Andrzej Kloczkowski:
Analysis of transcriptomic responses to SARS-CoV-2 reveals plausible defective pathways responsible for increased susceptibility to infection and complications and helps to develop fast-track repositioning of drugs against COVID-19. Comput. Biol. Medicine 149: 106029 (2022)- 2021
- [j17]Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan:
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 49(Database-Issue): D298-D308 (2021) - 2020
- [j16]Fran Sérgio Lobato, Gustavo Barbosa Libotte, Gustavo Mendes Platt, Andrzej Kloczkowski:
Identification of an Epidemiological Model to Simulate the COVID-19 Epidemic Using Robust Multiobjective Optimization and Stochastic Fractal Search. Comput. Math. Methods Medicine 2020: 9214159:1-9214159:8 (2020) - 2019
- [j15]Eshel Faraggi, A. Keith Dunker, Robert L. Jernigan, Andrzej Kloczkowski:
Entropy, Fluctuations, and Disordered Proteins. Entropy 21(8): 764 (2019) - 2018
- [j14]Óscar Álvarez, Juan Luis Fernández Martínez, Celia Fernández-Brillet, Ana Cernea, Zulima Fernández-Muñiz, Andrzej Kloczkowski:
Principal component analysis in protein tertiary structure prediction. J. Bioinform. Comput. Biol. 16(2): 1850005:1-1850005:34 (2018) - 2016
- [j13]Sumudu P. Leelananda, Andrzej Kloczkowski, Robert L. Jernigan:
Fold-specific sequence scoring improves protein sequence matching. BMC Bioinform. 17: 328 (2016) - [j12]Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram, Andrzej Kolinski:
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. BMC Bioinform. 17: 362 (2016) - [j11]Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski:
Predicting Designability of Small Proteins from Graph Features of Contact Maps. J. Comput. Biol. 23(5): 400-411 (2016) - 2015
- [j10]Vasily Sachnev, Saras Saraswathi, Rashid Niaz, Andrzej Kloczkowski, Suresh Sundaram:
Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer. BMC Bioinform. 16: 166:1-166:12 (2015) - 2014
- [j9]Pawel Gniewek, Andrzej Kolinski, Andrzej Kloczkowski, Dominik Gront:
BioShell-Threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinform. 15: 22 (2014) - 2012
- [j8]Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu:
P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics. J. Bioinform. Comput. Biol. 10(3) (2012) - 2011
- [j7]Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan:
MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles. BMC Bioinform. 12: 264 (2011) - 2010
- [j6]Yaping Feng, Andrzej Kloczkowski, Robert L. Jernigan:
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinform. 11: 92 (2010) - 2008
- [j5]Myron Peto, Andrzej Kloczkowski, Vasant G. Honavar, Robert L. Jernigan:
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. BMC Bioinform. 9 (2008) - 2007
- [j4]Haitao Cheng, Taner Z. Sen, Robert L. Jernigan, Andrzej Kloczkowski:
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). Bioinform. 23(19): 2628-2630 (2007) - 2006
- [j3]Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan:
Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinform. 7: 355 (2006) - 2005
- [j2]Taner Z. Sen, Robert L. Jernigan, Jean Garnier, Andrzej Kloczkowski:
GOR V server for protein secondary structure prediction. Bioinform. 21(11): 2787-2788 (2005) - 2004
- [j1]Taner Z. Sen, Andrzej Kloczkowski, Robert L. Jernigan, Changhui Yan, Vasant G. Honavar, Kai-Ming Ho, Cai-Zhuang Wang, Yungok Ihm, Haibo Cao, Xun Gu, Drena Dobbs:
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinform. 5: 205 (2004)
Conference and Workshop Papers
- 2024
- [c21]Saba Shahzadi, Mubashir Hassan, Andrzej Kloczkowski:
Bioinformatics Analysis Provides Insight into the Identification of miRNAs as Transcriptional Regulators in Respiratory Syncytial Virus Infection. IWBBIO (1) 2024: 49-62 - [c20]Saba Shahzadi, Mubashir Hassan, Muhammad Shahzad Iqbal, Zainab Yaseen, Andrzej Kloczkowski:
Bioinformatics-Based Analysis Provides a Deeper Understanding of How MicroRNAs Control Transcriptional Activity in Mumps Virus Infection. IWBBIO (2) 2024: 214-224 - [c19]Mubashir Hassan, Saba Shahzadi, Muhammad Yasir, Andrzej Kloczkowski:
Interpreting Respiratory Syncytial Virus (RSV) Nucleoprotein Mutations: A Structural and Functional Perspective. IWBBIO (2) 2024: 356-365 - 2023
- [c18]Andrzej Kloczkowski, Juan Luis Fernández Martínez, Zulima Fernández-Muñiz:
Computational Models for COVID-19 Dynamics Prediction. ICAISC (2) 2023: 228-238 - [c17]Óscar Álvarez-Machancoses, Eshel Faraggi, Enrique J. de Andrés-Galiana, Juan Luis Fernández Martínez, Andrzej Kloczkowski:
Prediction of Functional Effects of Protein Amino Acid Mutations. IWBBIO (2) 2023: 59-71 - [c16]Saba Shahzadi, Mubashir Hassan, Andrzej Kloczkowski:
Structural Analysis of RNA-Binding Protein EWSR1 Involved in Ewing's Sarcoma Through Domain Assembly and Conformational Molecular Dynamics Studies. IWBBIO (1) 2023: 181-190 - [c15]Mubashir Hassan, Saba Shahzadi, Andrzej Kloczkowski:
Pharmacoinformatic Analysis of Drug Leads for Alzheimer's Disease from FDA-Approved Dataset Through Drug Repositioning Studies. IWBBIO (1) 2023: 191-201 - 2020
- [c14]Óscar Álvarez-Machancoses, Enrique J. deAndrés-Galiana, Juan Luis Fernández Martínez, Andrzej Kloczkowski:
The Utilization of Different Classifiers to Perform Drug Repositioning in Inclusion Body Myositis Supports the Concept of Biological Invariance. ICAISC (1) 2020: 589-598 - [c13]Wei-Lun Alterovitz, Eshel Faraggi, Christopher J. Oldfield, Jingwei Meng, Bin Xue, Fei Huang, Pedro Romero, Andrzej Kloczkowski, Vladimir N. Uversky, A. Keith Dunker:
Many-to-One Binding by Intrinsically Disordered Protein Regions. PSB 2020: 159-170 - 2019
- [c12]Girik Malik, Anirban Banerji, Maksim Kouza, Irina Alexandra Buhimschi, Andrzej Kloczkowski:
Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths. IWBBIO (2) 2019: 245-258 - [c11]Michael T. Zimmermann, Fadi Towfic, Robert L. Jernigan, Andrzej Kloczkowski:
Characteristics of Protein Fold Space Exhibits Close Dependence on Domain Usage. IWBBIO (1) 2019: 356-369 - 2018
- [c10]Óscar Álvarez, Juan Luis Fernández Martínez, Celia Fernández-Brillet, Ana Cernea, Zulima Fernández-Muñiz, Andrzej Kloczkowski:
On the Use of Principal Component Analysis and Particle Swarm Optimization in Protein Tertiary Structure Prediction. ICAISC (2) 2018: 107-116 - [c9]Óscar Álvarez, Juan Luis Fernández Martínez, Ana Cernea, María Zulima Fernández-Muñiz, Andrzej Kloczkowski:
Protein Tertiary Structure Prediction via SVD and PSO Sampling. IWBBIO (1) 2018: 211-220 - 2015
- [c8]Sumudu P. Leelananda, Robert L. Jernigan, Andrzej Kloczkowski:
Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. RECOMB 2015: 188-201 - 2013
- [c7]Saras Saraswathi, B. S. Mahanand, Andrzej Kloczkowski, Suresh Sundaram, N. Sundararajan:
Detection of onset of Alzheimer's disease from MRI images using a GA-ELM-PSO classifier. CIMI 2013: 42-48 - 2011
- [c6]Yuanyuan Huang, Steve Bonett, Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu:
P.R.E.S.S. - An R-package for exploring residual-level protein structural statistics. BIBM Workshops 2011: 382-389 - [c5]Juan Luis Fernández Martínez, Esperanza García Gonzalo, Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski:
Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling. ICSI (1) 2011: 1-8 - 2010
- [c4]Michael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan:
Immunoglobulin functional motions and their effects on the complementarity determining regions. BCB 2010: 621-626 - [c3]Ataur R. Katebi, Pawel Gniewek, Michael T. Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan:
Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. BCB 2010: 653-655 - [c2]Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan:
An Extreme Learning Machine Classifier for Prediction of Relative Solvent Accessibility in Proteins. IJCCI (ICFC-ICNC) 2010: 364-369 - [c1]Saras Saraswathi, Robert L. Jernigan, Andrzej Kloczkowski, Andrzej Kolinski:
Protein Secondary Structure Prediction using Knowledge-based Potentials. IJCCI (ICFC-ICNC) 2010: 370-375
Parts in Books or Collections
- 2021
- [p1]Eshel Faraggi, Robert L. Jernigan, Andrzej Kloczkowski:
A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. Artificial Neural Networks, 3rd Edition 2021: 307-316
Editorship
- 2021
- [e1]Yufei Huang, Lukasz A. Kurgan, Feng Luo, Xiaohua Hu, Yidong Chen, Edward R. Dougherty, Andrzej Kloczkowski, Yaohang Li:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Houston, TX, USA, December 9-12, 2021. IEEE 2021, ISBN 978-1-6654-0126-5 [contents]
Coauthor Index
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