A new generalized Born model for estimating the free energy of hydration is presented. The new generalized Born/volume integral (GB/VI) estimates the free energy of hydration as a classical electrostatic energy plus a cavitation energy that is not based upon atomic surface area (SA) used in GB/SA hydration models but on a VI London dispersion energy estimated from quantities already calculated in the classical electrostatic energy. The (relatively few) GB/VI model parameters are fitted to experimental data, and parameterizations for two different atomic partial charge models are presented. Comparison of the calculated and experimental free energies of hydration for 560 small molecules (both neutral and charged) shows good agreement (r(2) = 0.94).
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms
Identification of folding preferences of cleavage junctions of HIV-1 precursor proteins for regulation of cleavability
Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis
Utilization of 6-(methylsulfinyl)hexyl isothiocyanate for sensitization of tumor cells to antitumor agents in combination therapies
Biotransformation of LASSBio-579 and pharmacological evaluation of p-hydroxylated metabolite a N-phenylpiperazine antipsychotic lead compound
Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: modulation of inhibition by heparin and design of mimetic inhibitors
The molecular basis for the selectivity of tadalafil toward phosphodiesterase 5 and 6: a modeling study
Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment
Pyrimidine nucleotides with 4-alkyloxyimino and terminal tetraphosphate δ-ester modifications as selective agonists of the P2Y(4) receptor
Discovery and structure-activity relationship of potent and selective covalent inhibitors of transglutaminase 2 for Huntington's disease
Interpreting the structural mechanism of action for MT7 and human muscarinic acetylcholine receptor 1 complex by modeling protein-protein interaction
Multiple sites in the N-terminal half of simian immunodeficiency virus capsid protein contribute to evasion from rhesus monkey TRIM5α-mediated restriction
A structural constraint for functional interaction between N-terminal and C-terminal domains in simian immunodeficiency virus capsid proteins
Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor
The atypical stimulant and nootropic modafinil interacts with the dopamine transporter in a different manner than classical cocaine-like inhibitors
The identification of a small molecule compound that reduces HIV-1 Nef-mediated viral infectivity enhancement
Discovery and computer aided potency optimization of a novel class of small molecule CXCR4 antagonists
APOBEC3G oligomerization is associated with the inhibition of both Alu and LINE-1 retrotransposition
Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies
The phosphorylation of HIV-1 Gag by atypical protein kinase C facilitates viral infectivity by promoting Vpr incorporation into virions
Combination of docking, molecular dynamics and quantum mechanical calculations for metabolism prediction of 3,4-methylenedioxybenzoyl-2-thienylhydrazone
Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models
Structural refinement of pyrazolo[4,3-d]pyrimidine derivatives to obtain highly potent and selective antagonists for the human A3 adenosine receptor
Methemoglobin Formation and Characterization of Hemoglobin Adducts of Carcinogenic Aromatic Amines and Heterocyclic Aromatic Amines
In silico identification of novel inhibitors against Plasmodium falciparum dihydroorate dehydrogenase
A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs
A binding mode hypothesis of tiagabine confirms liothyronine effect on γ-aminobutyric acid transporter 1 (GAT1)
Within-host co-evolution of Gag P453L and protease D30N/N88D demonstrates virological advantage in a highly protease inhibitor-exposed HIV-1 case
Defects in the calcium-binding region drastically affect the cadherin-like domains of RET tyrosine kinase
Dihydroxyacetone phosphate aldolase catalyzed synthesis of structurally diverse polyhydroxylated pyrrolidine derivatives and evaluation of their glycosidase inhibitory properties
PROTEIN STRUCTURE. Crystal structure of a mycobacterial Insig homolog provides insight into how these sensors monitor sterol levels
Structural changes of Listeria monocytogenes Sortase A: a key to understanding the catalytic mechanism
A novel pharmacophore model to identify leads for simultaneous inhibition of anti-coagulation and anti-inflammatory activities of snake venom phospholipase A(2)
Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory
Structure-guided minimalist redesign of the L-fuculose-1-phosphate aldolase active site: expedient synthesis of novel polyhydroxylated pyrrolizidines and their inhibitory properties against glycosidases and intestinal disaccharidases
Assessment of fully automated antibody homology modeling protocols in molecular operating environment
Green-lighting green fluorescent protein: faster and more efficient folding by eliminating a cis-trans peptide isomerization event
A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model
A computational approach predicting CYP450 metabolism and estrogenic activity of an endocrine disrupting compound (PCB-30)
Endocrine-disrupting potentials of equine estrogens equilin, equilenin, and their metabolites, in the medaka Oryzias latipes: in silico and DNA microarray studies
The study of dual COX-2/5-LOX inhibitors by using electronic-topological approach based on data on the ligand-receptor interactions
Characterization of interactions and pharmacophore development for DFG-out inhibitors to RET tyrosine kinase
The acetaminophen metabolite N-acetyl-p-benzoquinone imine (NAPQI) inhibits glutathione synthetase in vitro; a clue to the mechanism of 5-oxoprolinuric acidosis?
SU11248 (sunitinib) directly inhibits the activity of mammalian 5'-AMP-activated protein kinase (AMPK)
Synthesis and biological evaluation of colchicine C-ring analogues tethered with aliphatic linkers suitable for prodrug derivatisation
An N-terminal extension to the hepatitis B virus core protein forms a poorly ordered trimeric spike in assembled virus-like particles
Enzymatic characterization of in vitro-expressed Baikal seal cytochrome P450 (CYP) 1A1, 1A2, and 1B1: implication of low metabolic potential of CYP1A2 uniquely evolved in aquatic mammals
DOCKTITE-a highly versatile step-by-step workflow for covalent docking and virtual screening in the molecular operating environment
A computational approach to evaluate the androgenic affinity of iprodione, procymidone, vinclozolin and their metabolites
Nuclear Receptor-Like Structure and Interaction of Congenital Heart Disease-Associated Factors GATA4 and NKX2-5
A novel bifunctional hybrid with marine bacterium alkaline phosphatase and Far Eastern holothurian mannan-binding lectin activities
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
Classification of protein binding in hydroxyapatite chromatography: synergistic interactions on the molecular scale
Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections
Aromatic sulfonyl fluorides covalently kinetically stabilize transthyretin to prevent amyloidogenesis while affording a fluorescent conjugate
1,2,4-Triazolyl 5-Azaspiro[2.4]heptanes: Lead Identification and Early Lead Optimization of a New Series of Potent and Selective Dopamine D3 Receptor Antagonists
In silico identification of promiscuous scaffolds as potential inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase for treatment of Falciparum malaria
Discovery of Selective Inhibitors Targeting Acetylcholinesterase 1 from Disease-Transmitting Mosquitoes
Novel Potent Proline-Based Metalloproteinase Inhibitors: Design, (Radio)Synthesis, and First in Vivo Evaluation as Radiotracers for Positron Emission Tomography
Characterization of acetyl-CoA and propionyl-CoA carboxylases encoded by Leptospira interrogans serovar Lai: an initial biochemical study for leptospiral gluconeogenesis via anaplerotic CO(2) assimilation
Pyrimidine-Based Inhibitors of Dynamin I GTPase Activity: Competitive Inhibition at the Pleckstrin Homology Domain
Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors
Analyses of the Binding between Water Soluble C60 Derivatives and Potential Drug Targets through a Molecular Docking Approach
Carbohydrate-binding motifs in a novel type lectin from the sea mussel Crenomytilus grayanus: Homology modeling study and site-specific mutagenesis
A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments
An Innovative High-Throughput Screening Approach for Discovery of Small Molecules That Inhibit TNF Receptors
Binding position analysis of target proteins with the use of amidopyrene probes as LA-LDI enhancing tags
Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA
A Novel Interaction Between the TLR7 and a Colchicine Derivative Revealed Through a Computational and Experimental Study
Molecular architecture and the structural basis for anion interaction in prestin and SLC26 transporters
Mouse 11β-hydroxysteroid dehydrogenase type 2 for human application: homology modeling, structural analysis and ligand-receptor interaction
Extracting functional groups of ALLINI to design derivatives of FDA-approved drugs: Inhibition of HIV-1 integrase
Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis
The Genome of a Tortoise Herpesvirus (Testudinid Herpesvirus 3) Has a Novel Structure and Contains a Large Region That Is Not Required for Replication In Vitro or Virulence In Vivo
Deletion of a 197-Amino-Acid Region in the N-Terminal Domain of Spike Protein Attenuates Porcine Epidemic Diarrhea Virus in Piglets
Functional characterization of residues required for the herpes simplex virus 1 E3 ubiquitin ligase ICP0 to interact with the cellular E2 ubiquitin-conjugating enzyme UBE2D1 (UbcH5a)
A noncanonical mu-1A-binding motif in the N terminus of HIV-1 Nef determines its ability to downregulate major histocompatibility complex class I in T lymphocytes
Evaluation of influenza virus A/H3N2 and B vaccines on the basis of cross-reactivity of postvaccination human serum antibodies against influenza viruses A/H3N2 and B isolated in MDCK cells and embryonated hen eggs
Specific protein-labeling and ligand-binding position analysis with amidopyrene probes as LDI MS tags
Identification of small molecules uncoupling the Notch::Jagged interaction through an integrated high-throughput screening
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench
The systematic modeling studies and free energy calculations of the phenazine compounds as anti-tuberculosis agents
Molecular determinants of potent P2X2 antagonism identified by functional analysis, mutagenesis, and homology docking
In silico screening and surface plasma resonance-based verification of programmed death 1-targeted peptides
Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction
Structure-Based Virtual Screening of Pseudomonas aeruginosa LpxA Inhibitors Using Pharmacophore-Based Approach.
Identification of novel insect β-N-acetylhexosaminidase OfHex1 inhibitors based on virtual screening, biological evaluation, and molecular dynamics simulation.
Harmonic analysis of the fluorescence response of bimane adducts of colicin E1 at helices 6, 7, and 10.
Variable Region Identical IgA and IgE to Cryptococcus neoformans Capsular Polysaccharide Manifest Specificity Differences.
Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism
Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease
Structural, functional, and stability change predictions in human telomerase upon specific point mutations
Computer-aided drug design of small molecule inhibitors of the ERCC1-XPF protein-protein interaction
Open-channel blocking action of volatile anaesthetics desflurane and sevoflurane on human voltage-gated Kv 1.5 channel.
In silico design, synthesis and evaluation of 3'-O-benzylated analogs of salacinol, a potent α-glucosidase inhibitor isolated from an Ayurvedic traditional medicine "Salacia"
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization
In Silico Study of Alkaloids as α-Glucosidase Inhibitors: Hope for the Discovery of Effective Lead Compounds
The Dependence of Implicit Solvent Model Parameters and Electronic Absorption Spectra and Photoinduced Charge Transfer.
Design, synthesis and biological activity of selective hCAs inhibitors based on 2-(benzylsulfinyl)benzoic acid scaffold
Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions
Mutagenesis Studies and Structure-function Relationships for GalNAc/Gal-Specific Lectin from the Sea Mussel Crenomytilus grayanus
Indole-Based Hydrazones Containing A Sulfonamide Moiety as Selective Inhibitors of Tumor-Associated Human Carbonic Anhydrase Isoforms IX and XII
Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon
Novel Indole-Based Hydrazones as Potent Inhibitors of the α-class Carbonic Anhydrase from Pathogenic Bacterium Vibrio cholerae
Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus.
Synthesis, Docking, Computational Studies, and Antimicrobial Evaluations of New Dipeptide Derivatives Based on Nicotinoylglycylglycine Hydrazide.
Identifying the sarco(endo)plasmic reticulum Ca2+ ATPase (SERCA) as a potential target for hypericin--a theoretical study
GRID-independent molecular descriptor analysis and molecular docking studies to mimic the binding hypothesis of γ-aminobutyric acid transporter 1 (GAT1) inhibitors
Urate transporter inhibitor lesinurad is a selective peroxisome proliferator-activated receptor gamma modulator (sPPARγM) in vitro
Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity, and Molecular Dynamics Studies
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units
Practical spectrophotometric assay for the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase, a potential antibiotic target
Discovery of cyanopyridine scaffold as novel indoleamine-2,3-dioxygenase 1 (IDO1) inhibitors through virtual screening and preliminary hit optimisation
Amoebicidal effect of 5,5'-[(4-nitrophenyl)methylene]bis-6-hydroxy-2-mercapto-3-methyl-4(3H)-pyrimidinone), a new drug against Entamoeba histolytica.
Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
In silico and in vitro studies on the anti-cancer activity of andrographolide targeting survivin in human breast cancer stem cells.
Enhancing the activity of platinum-based drugs by improved inhibitors of ERCC1-XPF-mediated DNA repair
Determination of a T cell receptor of potent CD8+ T cells against simian immunodeficiency virus infection in Burmese rhesus macaques
Assessment of Risks of Dioxins for Aryl Hydrocarbon Receptor-Mediated Effects in Polar Bear (Ursus maritimus ) by in Vitro and in Silico Approaches
Potential inhibitors interacting in Neuropilin-1 to develop an adjuvant drug against COVID-19, by molecular docking.
In vivo and in silico analyses of estrogenic potential of equine estrogens in medaka (Oryzias latipes).
Calmodulin mutant in central linker reduces the binding affinity with PreIQ and IQ while interacting with CaV 1.2 channels
Development of photoaffinity derivatives of the antitumor macrolide aplyronine A, a PPI-inducer between actin and tubulin
S-(+)-Pentedrone and R-(+)-methylone as the most oxidative and cytotoxic enantiomers to dopaminergic SH-SY5Y cells: Role of MRP1 and P-gp in cathinones enantioselectivity.
Identification and characterization of the zosA gene involved in copper uptake in Bacillus subtilis 168
Multiple mutations in RNA polymerase β-subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory.
A Holistic Evolutionary and 3D Pharmacophore Modelling Study Provides Insights into the Metabolism, Function, and Substrate Selectivity of the Human Monocarboxylate Transporter 4 (hMCT4).
"Photo-Rimonabant": Synthesis and Biological Evaluation of Novel Photoswitchable Molecules Derived from Rimonabant Lead to a Highly Selective and Nanomolar "Cis-On" CB1R Antagonist.
Molecular docking and pharmacophore models to probe binding hypothesis of inhibitors of hypoxia inducible factor-1.
Engineering Cofactor Specificity of a Thermostable Phosphite Dehydrogenase for a Highly Efficient and Robust NADPH Regeneration System.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Evolution of Pluripotency
Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.
Lipidomics & Rhinovirus Infection
Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Torsion dystonia is a movement disorder characterized by loss of control of voluntary movements appearing as sustained muscle contractions and/or abnormal postures. Here is the latest research.
Generating Insulin-Secreting Cells
Reprogramming cells or using induced pluripotent stem cells to generate insulin-secreting cells has significant therapeutic implications for diabetics. Here is the latest research on generation of insulin-secreting cells.
Central Pontine Myelinolysis
Central Pontine Myelinolysis is a neurologic disorder caused most frequently by rapid correction of hyponatremia and is characterized by demyelination that affects the central portion of the base of the pons. Here is the latest research on this disease.
Epigenome editing is the directed modification of epigenetic marks on chromatin at specified loci. This tool has many applications in research as well as in the clinic. Find the latest research on epigenome editing here.