Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. - 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 (BMC Bioinform., 2004)

GOR V server for protein secondary structure prediction. - Taner Z. Sen; Robert L. Jernigan; Jean Garnier; Andrzej Kloczkowski (Bioinform., 2005)

Functional clustering of yeast proteins from the protein-protein interaction network. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2006)

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM). - Haitao Cheng; Taner Z. Sen; Robert L. Jernigan; Andrzej Kloczkowski (Bioinform., 2007)

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. - Myron Peto; Andrzej Kloczkowski; Vasant G. Honavar; Robert L. Jernigan (BMC Bioinform., 2008)

Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. - Ataur R. Katebi; Pawel Gniewek; Michael T. Zimmermann; Saras Saraswathi; Zhenming Gong; Christopher K. Tuggle; Andrzej Kloczkowski; Robert L. Jernigan (BCB, 2010)

Immunoglobulin functional motions and their effects on the complementarity determining regions. - Michael T. Zimmermann; Aris Skliros; Saras Saraswathi; Andrzej Kloczkowski; Robert L. Jernigan (BCB, 2010)

Protein Secondary Structure Prediction using Knowledge-based Potentials. - Saras Saraswathi; Robert L. Jernigan; Andrzej Kloczkowski; Andrzej Kolinski (IJCCI (ICFC-ICNC), 2010)

An Extreme Learning Machine Classifier for Prediction of Relative Solvent Accessibility in Proteins. - Saras Saraswathi; Andrzej Kloczkowski; Robert L. Jernigan (IJCCI (ICFC-ICNC), 2010)

Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. - Yaping Feng; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2010)

Particle Swarm Optimization: A Powerful Family of Stochastic Optimizers. Analysis, Design and Application to Inverse Modelling. - Juan Luis Fernández Martínez; Esperanza García Gonzalo; Saras Saraswathi; Robert L. Jernigan; Andrzej Kloczkowski (ICSI (1), 2011)

MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles. - Michael T. Zimmermann; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2011)

P.R.E.S.S. - an R-package for Exploring Residual-Level protein Structural Statistics. - Yuanyuan Huang 004; Steve Bonett; Andrzej Kloczkowski; Robert L. Jernigan; Zhijun Wu (J. Bioinform. Comput. Biol., 2012)

Detection of onset of Alzheimer's disease from MRI images using a GA-ELM-PSO classifier. - Saras Saraswathi; B. S. Mahanand; Andrzej Kloczkowski; Suresh Sundaram 002; N. Sundararajan 001 (CIMI, 2013)

BioShell-Threading: versatile Monte Carlo package for protein 3D threading. - Pawel Gniewek; Andrzej Kolinski; Andrzej Kloczkowski; Dominik Gront (BMC Bioinform., 2014)

Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models. - Sumudu P. Leelananda; Robert L. Jernigan; Andrzej Kloczkowski (RECOMB, 2015)

Multi-class BCGA-ELM based classifier that identifies biomarkers associated with hallmarks of cancer. - Vasily Sachnev; Saras Saraswathi; Rashid Niaz; Andrzej Kloczkowski; Suresh Sundaram 002 (BMC Bioinform., 2015)

Fold-specific sequence scoring improves protein sequence matching. - Sumudu P. Leelananda; Andrzej Kloczkowski; Robert L. Jernigan (BMC Bioinform., 2016)

Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach. - Shamima Rashid; Saras Saraswathi; Andrzej Kloczkowski; Suresh Sundaram 002; Andrzej Kolinski (BMC Bioinform., 2016)

Predicting Designability of Small Proteins from Graph Features of Contact Maps. - Sumudu P. Leelananda; Robert L. Jernigan; Andrzej Kloczkowski (J. Comput. Biol., 2016)

On the Use of Principal Component Analysis and Particle Swarm Optimization in Protein Tertiary Structure Prediction. - Óscar Álvarez; Juan Luis Fernández Martínez; Celia Fernández-Brillet; Ana Cernea; Zulima Fernández-Muñiz; Andrzej Kloczkowski (ICAISC (2), 2018)

Protein Tertiary Structure Prediction via SVD and PSO Sampling. - Óscar Álvarez; Juan Luis Fernández Martínez; Ana Cernea; María Zulima Fernández-Muñiz; Andrzej Kloczkowski (IWBBIO (1), 2018)

Principal component analysis in protein tertiary structure prediction. - Óscar Álvarez; Juan Luis Fernández Martínez; Celia Fernández-Brillet; Ana Cernea; Zulima Fernández-Muñiz; Andrzej Kloczkowski (J. Bioinform. Comput. Biol., 2018)

Deciphering General Characteristics of Residues Constituting Allosteric Communication Paths. - Girik Malik; Anirban Banerji; Maksim Kouza; Irina Alexandra Buhimschi; Andrzej Kloczkowski (IWBBIO (2), 2019)

Characteristics of Protein Fold Space Exhibits Close Dependence on Domain Usage. - Michael T. Zimmermann; Fadi Towfic; Robert L. Jernigan; Andrzej Kloczkowski (IWBBIO (1), 2019)

Entropy, Fluctuations, and Disordered Proteins. - Eshel Faraggi; A. Keith Dunker; Robert L. Jernigan; Andrzej Kloczkowski (Entropy, 2019)

The Utilization of Different Classifiers to Perform Drug Repositioning in Inclusion Body Myositis Supports the Concept of Biological Invariance. - Óscar Álvarez-Machancoses; Enrique J. deAndrés-Galiana; Juan Luis Fernández Martínez; Andrzej Kloczkowski (ICAISC (1), 2020)

Many-to-One Binding by Intrinsically Disordered Protein Regions. - Wei-Lun Alterovitz; Eshel Faraggi; Christopher J. Oldfield; Jingwei Meng; Bin Xue; Fei Huang; Pedro Romero; Andrzej Kloczkowski; Vladimir N. Uversky; A. Keith Dunker (PSB, 2020)

Identification of an Epidemiological Model to Simulate the COVID-19 Epidemic Using Robust Multiobjective Optimization and Stochastic Fractal Search. - Fran Sérgio Lobato; Gustavo Barbosa Libotte; Gustavo Mendes Platt; Andrzej Kloczkowski (Comput. Math. Methods Medicine, 2020)

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models. - Eshel Faraggi; Robert L. Jernigan; Andrzej Kloczkowski (Artificial Neural Networks, 3rd Edition, 2021)

DescribePROT: database of amino acid-level protein structure and function predictions. - 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; et al. (Nucleic Acids Res., 2021)

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. - Enrique J. deAndrés-Galiana; Juan Luis Fernández Martínez; Óscar Álvarez-Machancoses; Guillermina Bea; Carlos M. Galmarini; Andrzej Kloczkowski (Comput. Biol. Medicine, 2022)

Computational Models for COVID-19 Dynamics Prediction. - Andrzej Kloczkowski; Juan Luis Fernández Martínez; Zulima Fernández-Muñiz (ICAISC (2), 2023)

Prediction of Functional Effects of Protein Amino Acid Mutations. - Óscar Álvarez-Machancoses; Eshel Faraggi; Enrique J. de Andrés-Galiana; Juan Luis Fernández Martínez; Andrzej Kloczkowski (IWBBIO (2), 2023)

Pharmacoinformatic Analysis of Drug Leads for Alzheimer's Disease from FDA-Approved Dataset Through Drug Repositioning Studies. - Mubashir Hassan; Saba Shahzadi; Andrzej Kloczkowski (IWBBIO (1), 2023)

Structural Analysis of RNA-Binding Protein EWSR1 Involved in Ewing's Sarcoma Through Domain Assembly and Conformational Molecular Dynamics Studies. - Saba Shahzadi; Mubashir Hassan; Andrzej Kloczkowski (IWBBIO (1), 2023)

Machine Learning-Based Tool for Efficient Discrimination Between Deleterious and Neutral Missense Mutations. - Eshel Faraggi; Robert L. Jernigan; Andrzej Kloczkowski (ICAISC (3), 2024)

Interpreting Respiratory Syncytial Virus (RSV) Nucleoprotein Mutations: A Structural and Functional Perspective. - Mubashir Hassan; Saba Shahzadi; Muhammad Yasir; Andrzej Kloczkowski (IWBBIO (2), 2024)

Bioinformatics-Based Analysis Provides a Deeper Understanding of How MicroRNAs Control Transcriptional Activity in Mumps Virus Infection. - Saba Shahzadi; Mubashir Hassan; Muhammad Shahzad Iqbal; Zainab Yaseen; Andrzej Kloczkowski (IWBBIO (2), 2024)

Bioinformatics Analysis Provides Insight into the Identification of miRNAs as Transcriptional Regulators in Respiratory Syncytial Virus Infection. - Saba Shahzadi; Mubashir Hassan; Andrzej Kloczkowski (IWBBIO (1), 2024)