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1Coupled prediction of protein secondary and tertiary structure
J. Meiler, and D. Baker. Proceedings of the National Academy of Sciences, 100 (21): 12105â12110 (October 2003)
10 days ago by @scadsfct
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1Ligand-based virtual screen for the discovery of novel M5 inhibitor chemotypes
A. Geanes, H. Cho, K. Nance, K. McGowan, P. Conn, C. Jones, J. Meiler, and C. Lindsley. Bioorganic & Medicinal Chemistry Letters, 26 (18): 4487â4491 (September 2016)
10 days ago by @scadsfct
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1Sampling the conformational landscapes of transporters and receptors with AlphaFold2
D. del Alamo, D. Sala, H. Mchaourab, and J. Meiler. (November 2021)
10 days ago by @scadsfct
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1A unified hydrophobicity scale for multispan membrane proteins
J. Koehler, N. Woetzel, R. Staritzbichler, C. Sanders, and J. Meiler. Proteins: Structure, Function, and Bioinformatics, 76 (1): 13â29 (December 2008)
10 days ago by @scadsfct
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1BCL::Mol2Dâa robust atom environment descriptor for QSAR modeling and lead optimization
O. Vu, J. Mendenhall, D. Altarawy, and J. Meiler. Journal of Computer-Aided Molecular Design, 33 (5): 477â486 (April 2019)
10 days ago by @scadsfct
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1Neural Network Prediction of 13C NMR Chemical Shifts of Substituted Benzenes
J. Meiler, R. Meusinger, and M. Will. Monatshefte fÃ¼r Chemie / Chemical Monthly, 130 (9): 1089â1095 (September 1999)
10 days ago by @scadsfct
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1Improving quantitative structureâactivity relationship models using Artificial Neural Networks trained with dropout
J. Mendenhall, and J. Meiler. Journal of Computer-Aided Molecular Design, 30 (2): 177â189 (February 2016)
10 days ago by @scadsfct
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13D-QSAR CoMFA study of benzoxazepine derivatives as mGluR5 positive allosteric modulators
E. Lowe, A. Ferrebee, A. Rodriguez, P. Conn, and J. Meiler. Bioorganic & Medicinal Chemistry Letters, 20 (19): 5922â5924 (October 2010)
10 days ago by @scadsfct
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1General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps
B. Brown, J. Mendenhall, A. Geanes, and J. Meiler. Journal of Chemical Information and Modeling, 61 (2): 603â620 (January 2021)
10 days ago by @scadsfct
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1Application of machine learning approaches on quantitative structure activity relationships
M. Butkiewicz, R. Mueller, D. Selic, E. Dawson, and J. Meiler. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, (March 2009)
10 days ago by @scadsfct
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1GPU-accelerated machine learning techniques enable QSAR modeling of large HTS data
E. Lowe, M. Butkiewicz, N. Woetzel, and J. Meiler. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (May 2012)
10 days ago by @scadsfct
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1Bcl&#x2237;ChemInfo - Qualitative analysis of machine learning models for activation of HSD involved in Alzheimerâs Disease
M. Butkiewicz, E. Lowe, and J. Meiler. 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (May 2012)
10 days ago by @scadsfct
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1Fast Determination of 13C NMR Chemical Shifts Using Artificial Neural Networks
J. Meiler, R. Meusinger, and M. Will. Journal of Chemical Information and Computer Sciences, 40 (5): 1169â1176 (August 2000)
10 days ago by @scadsfct
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1Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks
A. Bleckmann, and J. Meiler. QSAR & Combinatorial Science, 22 (7): 722â728 (October 2003)
10 days ago by @scadsfct
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1Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database
M. Butkiewicz, E. Lowe, R. Mueller, J. Mendenhall, P. Teixeira, C. Weaver, and J. Meiler. Molecules, 18 (1): 735â756 (January 2013)
10 days ago by @scadsfct
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1Novel methods of automated structure elucidation based on 13C NMR spectroscopy
J. Meiler, and M. KÃ¶ck. Magnetic Resonance in Chemistry, 42 (12): 1042â1045 (October 2004)
10 days ago by @scadsfct
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1Improved prediction of trans-membrane spans in proteins using an artificial neural network
J. Koehler, R. Mueller, and J. Meiler. 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, (March 2009)
10 days ago by @scadsfct
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1Comparative analysis of machine learning techniques for the prediction of logP
E. Lowe, M. Butkiewicz, M. Spellings, A. Omlor, and J. Meiler. 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), (April 2011)
10 days ago by @scadsfct
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1Discovery of 2â(2âBenzoxazoyl amino)â4âArylâ5âCyanopyrimidine as Negative Allosteric Modulators (NAMs) of Metabotropic Glutamate Receptorâ5 (mGlu5): From an Artificial Neural Network Virtual Screen to an In Vivo Tool Compound
R. Mueller, E. Dawson, J. Meiler, A. Rodriguez, B. Chauder, B. Bates, A. Felts, J. Lamb, U. Menon, S. Jadhav and 9 other author(s). ChemMedChem, 7 (3): 406â414 (January 2012)
10 days ago by @scadsfct
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1NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction
A. Al-Fatlawi, N. Afrin, C. Ozen, N. Malekian, and M. Schroeder. Frontiers in Bioinformatics, (March 2022)
13 days ago by @scadsfct
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1Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances
S. Bolz, and M. Schroeder. Expert Opinion on Drug Discovery, 18 (9): 973–985 (July 2023)
13 days ago by @scadsfct
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1A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance
N. Malekian, A. Agrawal, T. Berendonk, A. Al-Fatlawi, and M. Schroeder. Scientific Reports, (May 2022)
13 days ago by @scadsfct
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1A community effort in SARS‐CoV‐2 drug discovery
J. Schimunek, P. Seidl, K. Elez, T. Hempel, T. Le, F. Noé, S. Olsson, L. Raich, R. Winter, H. Gokcan and 142 other author(s). Molecular Informatics, (November 2023)
13 days ago by @scadsfct
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1An interaction-based drug discovery screen explains known SARS-CoV-2 inhibitors and predicts new compound scaffolds
P. Schake, K. Dishnica, F. Kaiser, C. Leberecht, V. Haupt, and M. Schroeder. Scientific Reports, (June 2023)
13 days ago by @scadsfct
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1Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening
M. Adasme, S. Bolz, A. Al-Fatlawi, and M. Schroeder. Journal of Cheminformatics, (March 2022)
13 days ago by @scadsfct
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1Targeting ion channels with ultra-large library screening for hit discovery
K. Melancon, P. Pliushcheuskaya, J. Meiler, and G. Künze. Frontiers in Molecular Neuroscience, (January 2024)
13 days ago by @scadsfct
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1Ferric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency
R. Maniero, C. Picco, A. Hartmann, F. Engelberger, A. Gradogna, J. Scholz-Starke, M. Melzer, G. Künze, A. Carpaneto, N. von Wirén and 1 other author(s). Nature Communications, (January 2024)
13 days ago by @scadsfct
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1Similar Binding Modes of cGMP Analogues Limit Selectivity in Modulating Retinal CNG Channels via the Cyclic Nucleotide-Binding Domain
P. Pliushcheuskaya, S. Kesh, E. Kaufmann, S. Wucherpfennig, F. Schwede, G. Künze, and V. Nache. ACS Chemical Neuroscience, 15 (8): 1652–1668 (April 2024)
13 days ago by @scadsfct
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1Structural Studies on the Binding Mode of Bisphenols to PPARγ
A. Useini, I. Schwerin, G. Künze, and N. Sträter. Biomolecules, 14 (6): 640 (May 2024)
13 days ago by @scadsfct
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1Combining Rosetta Sequence Design with Protein Language Model Predictions Using Evolutionary Scale Modeling (ESM) as Restraint
M. Ertelt, J. Meiler, and C. Schoeder. ACS Synthetic Biology, 13 (4): 1085--1092 (2024)
14 days ago by @scadsfct
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ESM
combining
design
protein
rosetta
sequence
topic_lifescienceESMcombiningdesignproteinrosettasequence
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1MutationExplorer: a webserver for mutation of proteins and 3D visualization of energetic impacts
M. Philipp, C. Moth, N. Ristic, J. Tiemann, F. Seufert, A. Panfilova, J. Meiler, P. Hildebrand, A. Stein, D. Wiegreffe and 1 other author(s). Nucleic Acids Research, (2024)
14 days ago by @scadsfct
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3d
mutation
mutationexplorer
proteins
webserver
topic_lifescience3dmutationmutationexplorerproteinswebserver
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1Backbone chemical shift and secondary structure assignments for mouse siderocalin
J. Moeller, N. Bozhanova, M. Voehler, J. Meiler, and C. Schoeder. Biomolecular NMR Assignments, 18 (1): 79--84 (2024)
14 days ago by @scadsfct
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backbone_chemical_shift
mouse_siderocalin
secondary_structure_assignment
topic_lifesciencebackbone_chemical_shiftmouse_siderocalinsecondary_structure_assignment
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1Modifying immune responses to adeno-associated virus vectors by capsid engineering
M. Bentler, R. Hardet, M. Ertelt, D. Rudolf, D. Kaniowska, A. Schneider, F. Vondran, C. Schoeder, M. Delphin, J. Lucifora and 1 other author(s). Molecular Therapy-Methods & Clinical Development, (2023)
14 days ago by @scadsfct
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adeno_virus
capsid_engineering
immune
modifying
responses
topic_lifescienceadeno_viruscapsid_engineeringimmunemodifyingresponses
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1Content-adaptive generation and parallel compositing of volumetric depth images for responsive visualization of large volume data
A. Gupta, P. Incardona, P. Hunt, G. Reina, S. Frey, S. Gumhold, U. Günther, and I. Sbalzarini. (June 2022)
19 days ago by @scadsfct
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1Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences
D. Alamo, J. Meiler, and H. Mchaourab. (May 2022)
19 days ago by @scadsfct
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1Genomic events stratifying prognosis of early gastric cancer
C. Molinari, L. Solaini, F. Rebuzzi, G. Tedaldi, D. Angeli, E. Petracci, D. Prascevic, J. Ewald, E. Rahm, M. Canale and 9 other author(s). Gastric Cancer, 27 (6): 1189--1200 (November 2024)
20 days ago by @scadsfct
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topic_lifescience
area_bigdata
Prognosis
Pen;
EGC;
ARID1A
LRP1B
topic_lifesciencearea_bigdataPrognosisPen;EGC;ARID1ALRP1B
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1Federated Learning on Transcriptomic Data: Model Quality and Performance Trade-Offs
A. Hannemann, J. Ewald, L. Seeger, and E. Buchmann. Computational Science – ICCS 2024: 24th International Conference, Malaga, Spain, July 2–4, 2024, Proceedings, Part IV, page 279–293. Berlin, Heidelberg, Springer-Verlag, (2024)
21 days ago by @scadsfct
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area_responsibleai
Cell
Classification,
Disease
Federated
Learning,
Prognosis
Type
topic_lifesciencearea_responsibleaiCellClassification,DiseaseFederatedLearning,PrognosisType
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1SetQuence & SetOmic: Deep Set Transformer-based Representations of Cancer Multi-Omics
N. Jurenaite, D. León-Periñán, V. Donath, S. Torge, and R. Jäkel. 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), page 1-9. (August 2022)
a month ago by @scadsfct
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topic_federatedlearn
livinglab
topic_lifescience
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1SetQuence & SetOmic: Deep Set Transformers for Whole Genome and Exome Tumour Analysis
N. Jurenaite, D. León-Periñán, V. Donath, S. Torge, and R. Jäkel. BioSystems, (January 2024)
a month ago by @scadsfct
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livinglab
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1Efficient Raycasting of Volumetric Depth Images for Remote Visualization of Large Volumes at High Frame Rates
A. Gupta, U. Günther, P. Incardona, G. Reina, S. Frey, S. Gumhold, and I. Sbalzarini. 2023 IEEE 16th Pacific Visualization Symposium (PacificVis), 19, page 61�70. IEEE, (April 2023)
2 months ago by @scadsfct
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1Model-based autotuning of discretization methods in numerical simulations of partial differential equations
N. Khouzami, F. Michel, P. Incardona, J. Castrillon, and I. Sbalzarini. Journal of Computational Science, (January 2022)
2 months ago by @scadsfct
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1Roadmap on Deep Learning for Microscopy
G. Volpe, C. W�hlby, L. Tian, M. Hecht, A. Yakimovich, K. Monakhova, L. Waller, I. Sbalzarini, C. Metzler, M. Xie and 65 other author(s). (2023)
2 months ago by @scadsfct
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topic_physchemistry
topic_mathfoundation
topic_lifescience
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1Analysis of the Hamiltonian Monte Carlo genotyping algorithm on PROVEDIt mixtures including a novel precision benchmark
M. Susik, and I. Sbalzarini. Forensic Science International: Genetics, (2023)
2 months ago by @scadsfct
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topic_lifescience
DNA
HMC
Probabilistic
Validation,
genotyping,
mixtures,
topic_lifescienceDNAHMCProbabilisticValidation,genotyping,mixtures,
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1Computational Power of Particle Methods
J. Pahlke, and I. Sbalzarini. CoRR, (2023)
2 months ago by @scadsfct
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1Quantifying Molecular Dynamics within Complex Cellular Morphologies using LLSM?FRAP (Small Methods 6/2022)
H. Colin?York, J. Heddleston, E. Wait, N. Karedla, M. deSantis, S. Khuon, T. Chew, I. Sbalzarini, and M. Fritzsche. Small Methods, (June 2022)
2 months ago by @scadsfct
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1A portable C++ library for memory and compute abstraction on multi?core CPUs and GPUs
P. Incardona, A. Gupta, S. Yaskovets, and I. Sbalzarini. Concurrency and Computation: Practice and Experience, (July 2023)
2 months ago by @scadsfct
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1A Gaussian jump process formulation of the reaction�diffusion master equation enables faster exact stochastic simulations
T. Subic, and I. Sbalzarini. The Journal of Chemical Physics, (November 2022)
2 months ago by @scadsfct
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1A high-order fully Lagrangian particle level-set method for dynamic surfaces
L. Schulze, S. Veettil, and I. Sbalzarini. CoRR, (2023)
2 months ago by @scadsfct
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1Hamiltonian Monte Carlo with strict convergence criteria reduces run-to-run variability in forensic DNA mixture deconvolution
M. Susik, H. Schönborn, and I. Sbalzarini. Forensic Science International: Genetics, (September 2022)
2 months ago by @scadsfct
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1Proven Distributed Memory Parallelization of Particle Methods
J. Pahlke, and I. Sbalzarini. (Sep 18, 2024)
2 months ago by @scadsfct
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topic_lifescience
algorithmics,
algorithms,
bounds,
definition,
distributed
engineering
formal
memory,
meshfree
methods,
parallelization,
particle
scalability
simulation
software
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