Ram Samudrala's publications related to therapeutic discovery
These are our publications related to therapeutic discovery. See
also a complete list of
our publications chronologically ordered or a list organised by areas of
research.
- Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls
Z, Samudrala R, Pohl J, Knight PR, Sambhara S. Antiviral
approaches against influenza virus. Clinical Microbiology
Reviews e0004022, 2023. in press
- Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S,
Aalinkeel R, Mahajan SD, Samudrala R. Multiscale analysis and validation of
effective drug combinations targeting driver KRAS mutations in
non-small cell lung cancer. International Journal of
Molecular Sciences 24: 997, 2023. *
- Mangione W, Falls Z, Samudrala R. Optimal
COVID-19 therapeutic candidate discovery using the CANDO
platform. Frontiers in Pharmacology 13: 970494,
2022. *
- Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao
M, Samudrala R. Identifying
protein features and pathways responsible for toxicity using machine
learning and tox21: Implications for predictive
toxicology. Molecules 27: 3021, 2022. *
- Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu
J, Broderick G, Sethi S, Samudrala R. Proteomic
network analysis of bronchoalveolar lavage fluid in ex-smokers to
discover implicated protein targets and novel drug treatments for
chronic obstructive pulmonary
disease. Pharmaceuticals 15: 566, 2022. *
- Falls Z, Fine J, Chopra G, Samudrala R. Accurate
prediction of inhibitor binding to HIV-1 protease using
CANDOCK. Frontiers in Chemistry 9: 775513, 2022.
- Schuler J, Falls Z, Mangione W, Hudson M, Bruggemann L,
Samudrala R. Evaluating
performance of drug repurposing technologies. Drug
Discovery Today 27: 49-64, 2022. *
- Overhoff B, Falls Z, Mangione W, Samudrala R. A
deep-learning proteomic-scale approach for drug
design. Pharmaceuticals (Basel) 14: 1277, 2021. *
- Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R,
Stavrou S, Melendy T. A
fluorescence-based, gain-of-signal, live cell system to evaluate
SARS-CoV-2 main protease inhibition. Antiviral
Research 195: 105183, 2021.
- Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M,
Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T,
Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G,
Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein
mimetic amyloid inhibitor potently abrogates cancer-associated
mutant p53 aggregation and restores tumor suppressor
function. Nature Communications 12: 3962, 2021.
- Hudson ML, Samudrala R. Multiscale
virtual screening optimization for shotgun drug repurposing using
the CANDO platform. Molecules 26: 2581-2597, 2021.
- Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ,
Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA,
Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL. A
synthetic small molecule stalls pre-mRNA splicing by promoting an
early-stage U2AF2-RNA complex. Cell Chemical Biology
28: 1145-1157, 2021.
- Mangione W, Falls Z, Chopra G, Samudrala R. cando.py:
Open source software for predictive bioanalytics of large scale
drug-protein-disease data. Journal of Chemical Information
and Modeling 60: 4131-4136, 2020. *
- Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R.
Shotgun
drug repurposing biotechnology to tackle epidemics and
pandemics. Drug Discovery Today 25: 1126-1128,
2020. *
- Fine J, Konc J, Samudrala R, Chopra G. CANDOCK:
Chemical Atomic Network-Based Hierarchical Flexible Docking
Algorithm Using Generalized Statistical
Potentials. Journal of Chemical Information and
Modeling 60: 1509-1527, 2020. *
- Fine J, Lackner R, Samudrala R, Chopra G. Computational
chemoproteomics to understand the role of selected psychoactives in
treating mental health indications. Scientific
Reports 9, 1315, 2019. *
- Schuler J, Samudrala R. Fingerprinting
CANDO: Increased accuracy with structure and ligand based shotgun
drug repurposing. ACS Omega 4: 17393-17403, 2019.
*
- Schuler J, Mangione W, Samudrala R, Ceusters W. Foundations
for a realism-based drug repurposing ontology. Proceedings of
the 10th International Conference on Biomedical Ontology, 2019.
- Falls Z, Mangione W, Schuler J, Samudrala R. Exploration
of interaction scoring criteria in the CANDO platform. BMC
Research Notes 12: 318, 2019. *
- Mangione W, Samudrala R. Identifying protein features
responsible for improved drug repurposing accuracies using the CANDO
platform: Implications for drug design. Molecules 24: 167,
2019. *
- Schuler J, Hudson M, Schwartz D, Samudrala R. A
systematic review of computational drug discovery, development, and
repurposing for Ebola Virus Disease Treatment. Molecules
22: E1777, 2017.
- Chopra C, Kaushik S, Elkin PL, Samudrala R. Combating
Ebola with repurposed therapeutics using the CANDO
platform. Molecules 21: 1537, 2016. *
- Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK,
Subramanian S, Samudrala R, Van Voorhis WC. Mycobacterium
cytidylate kinase appears to be an undruggable target. Journal
of Biomolecular Design 21: 695-700, 2016.
- Chopra G, Samudrala R. Exploring polypharmacology in
drug discovery and repurposing using the CANDO
platform. Current Pharmaceutical Design 22: 3109-3123
2016.
- Manocheewa S, Mittler JE, Samudrala R, Mullins
JI. Composite sequence-structure stability models as screening tools
for identifying vulnerable targets for HIV drug and vaccine
development. Viruses 7: 5718-5735, 2015.
- Sethi G, Chopra G, Samudrala R. Multiscale
modelling of relationships between protein classes and drug behavior
across all diseases using the CANDO platform. Mini Reviews
in Medicinal Chemistry, 15: 705-717, 2015.
- Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K,
Samudrala R. CANDO and
the infinite drug discovery frontier. Drug Discovery
Today 19: 1353-1363, 2014. *
- Lertkiatmongkol P, Assawamakin A, White G, Chopra G,
Rongnoparut P, Samudrala R, Tongsima S. Distal effect of
amino acid substitutions in CYP2C9 polymorphic variants causes
differences in interatomic interactions against
(S)-warfarin. PLoS One 8: e74053, 2013.
- Strategic protein target analysis for developing drugs to stop
dental caries. Horst JA, Pieper U, Sali A, Zhan L, Chopra G,
Samudrala R, Featherstone JD. Advances in Dental
Research 24: 86-93, 2012. *
- Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational
multitarget drug discovery. Polypharmacology
263-301, 2012. *
- Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E,
Samudrala R, Isern S, Michael SF. Viral
entry inhibitors block dengue antibody-dependent enhancement in
vitro. Antiviral Research 89: 71-74 2010. *
- Movahedzadeh F, Balaubramanian V, Bernard B,
Iyer S, Samudrala R, Franzblau SG, Balganesh TS.
Anti-tuberculosis agents: A rational approach for discovery and
development. Genomic and computational tools for emerging
infectious diseases, 2010.
- Costin JM, Jenwitheesuk E, Lok S-M, Hunsperger E, Conrads KA,
Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R,
Michael SF. Structural optimization and de novo design of
dengue virus entry inhibitory peptides. PLoS Neglected Tropical
Diseases 4: e721, 2010. *
- Bernard B, Samudrala R. A
generalized knowledge-based discriminatory function for biomolecular
interactions. Proteins: Structure, Function, and
Bioinformatics 76: 115-128, 2009.
- Jenwitheesuk E, Horst JA, Rivas K, Van Voorhis WC, Samudrala
R. Novel paradigms
for drug discovery: Computational multitarget
screening. Trends in Pharmacological Sciences 29:
62-71, 2008. [Accompanying cover.] *
- Samudrala R, Jenwitheesuk E. Identification of potential HIV-1
targets of minocycline. Bioinformatics 23:
2797-2799, 2007.
- Wang K, Mittler J, Samudrala R. Comment on "Evidence for
positive epistatis in HIV-1". Science 312: 848b,
2006.
- Jenwitheesuk E, Samudrala R. Identification of potential
multitarget antimalarial drugs. Journal of the American
Medical Association 294: 1490-1491, 2005. *
- Jenwitheesuk E, Samudrala R. Heptad-repeat-2 mutations
enhance the stability of the enfuvirtide-resistant HIV-1 gp41
hairpin structure. Antiviral Therapy 10: 893-900,
2005. *
- Jenwitheesuk E, Wang K, Mittler J, Samudrala R.
PIRSpred: A webserver for
reliable HIV-1 protein-inhibitor resistance/susceptibility
prediction. Trends in Microbiology 13: 150-151,
2005.
- Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1
protease inhibitors against human cytomegalovirus protease using
docking and molecular dynamics. AIDS 19: 529-533,
2005.
- Jenwitheesuk E, Samudrala R. Prediction of HIV-1
protease inhibitor resistance using a protein-inhibitor flexible
docking approach. Antiviral Therapy 10: 157-166,
2005.
- Jenwitheesuk E, Wang K, Mittler J, Samudrala R. Improved accuracy of HIV-1
genotypic susceptibility interpretation using a consensus
approach. AIDS 18: 1858-1859, 2004.
- Jenwitheesuk E, Samudrala R. Identifying inhibitors of
the SARS coronavirus proteinase. Bioorganic & Medicinal
Chemistry Letters 13: 3989-3992, 2003. [Most Cited Paper
2003 - 2006 Award.] *
- Jenwitheesuk E, Samudrala R. Improved prediction of
HIV-1 protease-inhibitor binding energies by molecular dynamics
simulations. BMC Structural Biology 3: 2, 2003. *
- Wang K, Jenwitheesuk E, Samudrala R, Mittler J. Simple linear model
provides highly accurate genotypic predictions of HIV-1 drug
resistance. Antiviral Therapy 9: 343-352, 2004.
- Wang K, Samudrala R, Mittler J. Weak
agreement between predictions of ``reduced susceptibility'' from
Antivirogram and PhenoSense assays. Journal of Clinical
Microbiology 42: 2353-2354, 2004.
- Wang K, Samudrala R, Mittler J. HIV-1
genotypic drug resistance interpretation algorithms need to include
hypersusceptibility mutations. Journal of Infectious
Diseases 190: 2055-2056, 2004.
- Wang K, Samudrala R, Mittler J. Antivirogram
or PhenoSense: a comparison of their reproducibility and an analysis
of their correlation. Antiviral Therapy 9: 703-712,
2004.
- Protein inhibitor
resistance/susceptibility prediction (PIRSpred) web server
module
- Computational
analysis of novel drug opportunities (CANDO) platform
Samudrala Computational Biology Research Group (CompBio) ||
admin@compbio.org