Publications by authors named "Alfonso T García-Sosa"

39Publications

Repurposing old drugs to fight multidrug resistant cancers.

Drug Resist Updat 2020 09 25;52:100713. Epub 2020 Jun 25.

Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria.

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http://dx.doi.org/10.1016/j.drup.2020.100713DOI Listing
September 2020

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity.

Environ Health Perspect 2020 02 7;128(2):27002. Epub 2020 Feb 7.

National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, North Carolina, USA.

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http://dx.doi.org/10.1289/EHP5580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064318PMC
February 2020

Structural insights and binding analysis for determining the molecular bases for programmed cell death protein ligand-1 inhibition.

Medchemcomm 2019 Oct 29;10(10):1810-1818. Epub 2019 Jul 29.

Research Institute for Medicines (iMed.ULisboa) , Faculty of Pharmacy , Universidade de Lisboa , 1649-003 Lisbon , Portugal . Email:

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http://dx.doi.org/10.1039/c9md00326fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839816PMC
October 2019

The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from may be Involved in the Resistance to Drugs such as Paromomycin.

Biomolecules 2019 11 11;9(11). Epub 2019 Nov 11.

Department of Microbiology and Parasitology, ISTUN Institute of Tropical Health, University of Navarra, IdiSNA (Navarra Institute for Health Research). Pamplona, E-31008 Navarra, Spain.

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http://dx.doi.org/10.3390/biom9110723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920834PMC
November 2019

Benford's law in medicinal chemistry: Implications for drug design.

Future Med Chem 2019 09;11(17):2247-2253

Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia.

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http://dx.doi.org/10.4155/fmc-2019-0006DOI Listing
September 2019

Data Mining and Machine Learning Models for Predicting Drug Likeness and Their Disease or Organ Category.

Front Chem 2018 9;6:162. Epub 2018 May 9.

Department of Molecular Technology, Institute of Chemistry, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.3389/fchem.2018.00162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5954128PMC
May 2018

Designing Ligands for Leishmania, Plasmodium, and Aspergillus N-Myristoyl Transferase with Specificity and Anti-Target-Safe Virtual Libraries.

Curr Comput Aided Drug Des 2018 ;14(2):131-141

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.

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http://dx.doi.org/10.2174/1573409914666180308163231DOI Listing
October 2018

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

J Comput Aided Mol Des 2018 01 6;32(1):211-224. Epub 2017 Sep 6.

Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.

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http://dx.doi.org/10.1007/s10822-017-0056-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767205PMC
January 2018

Chemical structure and correlation analysis of HIV-1 NNRT and NRT inhibitors and database-curated, published inhibition constants with chemical structure in diverse datasets.

J Mol Graph Model 2017 09 24;76:205-223. Epub 2017 Jun 24.

Institute of Chemistry, University of Tartu, Tartu 50411, Estonia. Electronic address:

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http://dx.doi.org/10.1016/j.jmgm.2017.06.019DOI Listing
September 2017

Optimization of in vivo DNA delivery with NickFect peptide vectors.

J Control Release 2016 11 21;241:135-143. Epub 2016 Sep 21.

Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu, Nooruse, 50411 Tartu, Estonia; Department of Neurochemistry, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden.

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http://dx.doi.org/10.1016/j.jconrel.2016.09.022DOI Listing
November 2016

Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets.

Molecules 2016 May 5;21(5). Epub 2016 May 5.

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.

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http://dx.doi.org/10.3390/molecules21050589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274217PMC
May 2016

Virtual Screening for HIV Protease Inhibitors Using a Novel Database Filtering Procedure.

Mol Inform 2015 06 22;34(6-7):485-92. Epub 2015 Jun 22.

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu, 50411, Estonia.

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http://dx.doi.org/10.1002/minf.201400170DOI Listing
June 2015

Improving the use of ranking in virtual screening against HIV-1 integrase with triangular numbers and including ligand profiling with antitargets.

J Chem Inf Model 2014 Nov 23;54(11):3172-85. Epub 2014 Oct 23.

Institute of Chemistry, University of Tartu , Ravila14a, Tartu 50411, Estonia.

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http://dx.doi.org/10.1021/ci500300uDOI Listing
November 2014

Peptide-ligand binding modeling of siRNA with cell-penetrating peptides.

Biomed Res Int 2014 24;2014:257040. Epub 2014 Jul 24.

Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia ; Department of Neurochemistry, Stockholm University, 106 91 Stockholm, Sweden.

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http://dx.doi.org/10.1155/2014/257040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131515PMC
September 2015

Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies.

J Chem Inf Model 2013 Jun 23;53(6):1388-405. Epub 2013 May 23.

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.

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http://pubs.acs.org/doi/10.1021/ci3005786
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http://dx.doi.org/10.1021/ci3005786DOI Listing
June 2013

DrugLogit: logistic discrimination between drugs and nondrugs including disease-specificity by assigning probabilities based on molecular properties.

J Chem Inf Model 2012 Aug 7;52(8):2165-80. Epub 2012 Aug 7.

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.

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http://dx.doi.org/10.1021/ci200587hDOI Listing
August 2012

Disease-Specific Differentiation Between Drugs and Non-Drugs Using Principal Component Analysis of Their Molecular Descriptor Space.

Mol Inform 2012 May 3;31(5):369-83. Epub 2012 May 3.

Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia phone: (+372) 7375254; fax: (+372) 7375264.

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http://dx.doi.org/10.1002/minf.201100094DOI Listing
May 2012

Combined approach using ligand efficiency, cross-docking, and antitarget hits for wild-type and drug-resistant Y181C HIV-1 reverse transcriptase.

J Chem Inf Model 2011 Oct 15;51(10):2595-611. Epub 2011 Sep 15.

Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.

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http://pubs.acs.org/doi/abs/10.1021/ci200203h
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http://dx.doi.org/10.1021/ci200203hDOI Listing
October 2011

Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex.

Mol Inform 2010 Sep 30;29(8-9):589-600. Epub 2010 Aug 30.

Curtin Health Innovation Research Institute, Western Australian Biomedical Research Institute, School of Biomedical Sciences and School of Pharmacy, Curtin University of Technology, GPO Box U1987, Perth WA 6865, Australia.

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http://dx.doi.org/10.1002/minf.201000007DOI Listing
September 2010

Drug efficiency indices for improvement of molecular docking scoring functions.

J Comput Chem 2010 Jan;31(1):174-84

Institute of Chemistry, University of Tartu, Jakobi 2, Tartu 51014, Estonia.

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http://dx.doi.org/10.1002/jcc.21306DOI Listing
January 2010

Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant.

J Chem Inf Model 2008 Oct 11;48(10):2074-80. Epub 2008 Oct 11.

Institute of Chemistry, University of Tartu, Jakobi 2-319, Tartu, Estonia.

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http://pubs.acs.org/doi/abs/10.1021/ci800242z
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http://dx.doi.org/10.1021/ci800242zDOI Listing
October 2008

Structure-based calculation of drug efficiency indices.

Bioinformatics 2007 Oct 5;23(20):2678-85. Epub 2007 Sep 5.

Institute of Chemical Physics, University of Tartu, 2 Jakobi Street, 51014 Tartu, Estonia.

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http://dx.doi.org/10.1093/bioinformatics/btm431DOI Listing
October 2007

The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

J Mol Model 2006 Mar 23;12(4):422-31. Epub 2005 Dec 23.

Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.

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http://dx.doi.org/10.1007/s00894-005-0063-1DOI Listing
March 2006

Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A.

Bioorg Med Chem 2006 Jan 3;14(2):395-408. Epub 2005 Oct 3.

Computer-Aided Molecular Design Laboratory, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S096808960500771
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http://dx.doi.org/10.1016/j.bmc.2005.08.018DOI Listing
January 2006

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

J Chem Inf Model 2005 May-Jun;45(3):624-33

Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK.

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http://dx.doi.org/10.1021/ci049694bDOI Listing
October 2005

The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models.

J Comput Aided Mol Des 2004 Feb;18(2):89-100

De Novo Pharmaceuticals, Compass House, Vision Park, Chivers Way, Histon, Cambridge CB4 9ZR, UK.

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http://dx.doi.org/10.1023/b:jcam.0000030032.81753.b4DOI Listing
February 2004

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

J Mol Model 2003 Jun 17;9(3):172-82. Epub 2003 May 17.

Department of Pharmacology, University of Cambridge, Tennis Court Road, CB2 1PD, Cambridge, UK.

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http://dx.doi.org/10.1007/s00894-003-0129-xDOI Listing
June 2003