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Current Opinion in Structural Biology, ISSN 0959-440X, 04/2018, Volume 49, pp. 139 - 144
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 02/2018, Volume 58, Issue 2, pp. 287 - 296
Journal Article
Current Topics in Medicinal Chemistry, ISSN 1568-0266, 2017, Volume 17, Issue 23, pp. 2617 - 2625
Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs) were first released to the public in the early 2009 with the code ACEMD.... 
Perspective | Simulation | Molecular dynamics | ACEMD | Drug discovery | Review | GPU | CHEMISTRY, MEDICINAL | DOCKING | GPCR-LIGAND RECOGNITION | RECEPTOR | PERCEPTION | PROFILE | FORCE-FIELD | SIMULATIONS | PROTEINS | FREE-ENERGY | BINDING | Time | Sampling | Graphics processing units
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 02/2018, Volume 58, Issue 2, pp. 287 - 296
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 02/2018, Volume 58, Issue 2, p. 287
Accurately predicting protein-ligand binding affinities is an important problem in computational chemistry since it can substantially accelerate drug discovery... 
Binding | State of the art | Correlation coefficients | 3-D technology | Artificial neural networks | Scoring | Computational chemistry | Chemistry | Neural networks | Predictions | Ligands | Affinity | Coordination compounds
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 07/2017, Volume 57, Issue 7, p. 1511
Protein preparation is a critical step in molecular simulations that consists of refining a Protein Data Bank (PDB) structure by assigning titration states and... 
Proteins | Molecules | Hydrogen storage | Simulation | Hydrogen bonds | Molecular dynamics | Chemical bonds | Protonation | Software | Titration | Hydrogen bonding
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2017, Volume 13, Issue 9, pp. 4003 - 4011
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 03/2019, Volume 59, Issue 3, pp. 1172 - 1181
Drug discovery suffers from high attrition because compounds initially deemed as promising can later show ineffectiveness or toxicity resulting from a poor... 
METABOLOMICS | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | CROSS-VALIDATION | COMPUTER SCIENCE, INFORMATION SYSTEMS | TRENDS | CHEMISTRY, MULTIDISCIPLINARY | DISCOVERY | PREDICTION | Neural networks | Toxicity | Normalizing
Journal Article
Bioinformatics, ISSN 1367-4803, 04/2019, Volume 35, Issue 7, pp. 1237 - 1238
Abstract Summary Virtual screening pipelines are one of the most popular used tools in structure-based drug discovery, since they can can reduce both time and... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DOCKING | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
Journal Article
CHEMICAL SCIENCE, ISSN 2041-6520, 12/2019, Volume 10, Issue 47, pp. 10911 - 10918
The capability to rank different potential drug molecules against a protein target for potency has always been a fundamental challenge in computational... 
SCORING FUNCTION | DESIGN | LIGAND-BINDING | DATABASE | ACCURATE DOCKING | DRUG DISCOVERY | CROSS-VALIDATION | BINDING-AFFINITY PREDICTION | INHIBITORS | CHEMISTRY, MULTIDISCIPLINARY | FREE-ENERGY PERTURBATION
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 03/2018, Volume 58, Issue 3, p. 683
Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening... 
Binding | Computer simulation | Research & development--R&D | Fragments | Molecular dynamics | Markov chains | Pharmacology | Molecular chains | Fragmentation | Studies | Proteins | Organic chemistry | Screening | Ligands | Affinity | Leverage | Kinetics
Journal Article
ISSN 2041-6520, 12/2019, Volume 1, Issue 47, pp. 1911 - 1918
The capability to rank different potential drug molecules against a protein target for potency has always been a fundamental challenge in computational... 
Journal Article
Bioinformatics, ISSN 1367-4803, 01/2019, Volume 35, Issue 2, pp. 243 - 250
Abstract Motivation Structure-based drug discovery methods exploit protein structural information to design small molecules binding to given protein pockets.... 
SITES | PROTEIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DOCKING | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2017, Volume 13, Issue 9, p. 4003
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of... 
Proteins | Simulation | Molecular dynamics | Molecular chains
Journal Article
Journal of Chemical Information and Modeling, ISSN 1549-9596, 03/2018, Volume 58, Issue 3, pp. 683 - 691
Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening... 
CHEMISTRY, MEDICINAL | DOCKING | DRUG DISCOVERY | COMPUTER SCIENCE, INFORMATION SYSTEMS | CXCR4 | CHEMISTRY, MULTIDISCIPLINARY | DYNAMICS SIMULATIONS | PROTEIN-BINDING SITES | IMPACT | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | CHEMOKINE | OPTIMIZATION | HIV-1 INFECTION | FORCE-FIELD PARAMETERIZATION
Journal Article
Journal of chemical information and modeling, 12/2018
Drug discovery suffers from high attrition as compounds initially deemed as promising can later show ineffectiveness or toxicity due to a poor understanding of... 
Journal Article
Current topics in medicinal chemistry, 2017, Volume 17, Issue 23, p. 2617
Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs) were first released to the public in the early 2009 with the code ACEMD.... 
Computer Graphics | Drug Discovery | Molecular Dynamics Simulation
Journal Article
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