Computer Aided Drug Design contract research services, Flexible molecular docking software. Drug Discovery virtual screening services. Computational chemistry in-silico tools. Molecular simulation and Molecular Dynamics technology. Receptor Structure Based Drug design. Bioinformatics. Drug design computer predictive programs. Post - QSAR Protein-Ligand and Protein-Protein interactions studies. Molecular Modelling. Inhibition. Research of Macromolecules' conformational changes

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Please point your browser to our new home page. 1E9M - Validate computations activation folded folding 1E9M - Moving properties assays services inhibition 1E9M - Assays building pka solution outsourcing marker 1E9M - Ic50, 1E9M - Inhibitory concentration 50%, 1E9M - New inhibitor, determinations of receptor binding affinity of a ligand, 1E9M - Competitive binding curve, the concentration required for 50% inhibition, 1E9M - Median inhibitory concentration, novel ligand, binding constant, 1E9M - Competitive inhibition, affinity, activators, agonists, antagonists, 1E9M - Activator, agonist, inhibition constant, inhibit, blocks, 1E9M - Interact, free binding energy, complex, measured pkd values, ki, 1E9M - Value pki, experiments, estimation, database, list, invitro, 1E9M - In-vitro, biological, chemical, measurement, inhibitors, ligands, 1E9M - Blockator, biochemical processes, anti , biologics, on-line, web based, 1E9M - Internet based, article, publications, docked, screened, tested, 1E9M - Checked, validated, complexed, protein/small molecule, 1E9M - Protein-ligand complex, research, dissolution dissociation constant, 1E9M - Mechanisms inhibits inhibited, constant of dissosiation, ki, pki, pkd 1E9M - Docking 1E9M - Virtual in silico screening, 1E9M - Insilico, hit identification, optimisation, calculations, 1E9M - Modelling, service provider, software, qsar study studies, 1E9M - Tool, scoring function, discovery, flexible docking, 1E9M - Competitive inhibition, affinity, activators, agonists, 1E9M - Antagonists, activator, agonist, , inhibition constant, 1E9M - Assay, 1E9M - Array, ic50, free binding energy, complex, measured pkd values, 1E9M - Value pki, optimization, de novo drug design, computer aided drug discovery, 1E9M - Experiments, biological activity, bioactivity, measurement, estimation, prediction, 1E9M - Hts, uhts, high throughput screening, ultra high-throughput screening, 1E9M - Training set, in silico, development, assessment, binding energy prediction, 1E9M - Three-dimensional quantitative structure activity relationship methods, 1E9M - Automatic docking, dock, 1E9M - Ic50 assays 1E9M - (assays to determine the concentration of a drug-like compound resulting in a 50% reduction in activity of a disease target), 1E9M - Serial dilutions of dmso compound libraries, indirect response models, 1E9M - Sc50 (drug concentration eliciting 50% of the maximum stimulation), 1E9M - In vitrotest platform technology, picomolar, prodrugs detection insilico, 1E9M - Small molecule drug discovery, disease therapeutic target protein, 1E9M - Docking simulation, predictive model, cadd, camm, qm, 1E9M - Homology modeling and docking studies of, 1E9M - Case study, 1E9M - Validation free energy, score, automated docking and scoring of flexible ligands to receptors, 1E9M - Recognition of ligands by their receptors, educational research software tool, 1E9M - Conventional computational methods, sampling of barrier-crossing events, determined, 1E9M - Functional form and parameter sets used, to describe the interactions (potential, forces), 1E9M - System of particles (atoms or similarly sized objects), electron configuration, numerical field, quantum chemical, 1E9M - Heuristic, force fields, energy refinement, 1E9M - Model building, define, mutant 1E9M - Forcefield molecular simulation package, 1E9M - Study of biomolecular systems, application to aqueous or apolar solutions of proteins, 1E9M - Nucleotides and sugars, second-generation forcefields, 1E9M - The description of the electronic behavior of atoms and molecules, reactivity, one of the applications of quantum chemistry 1E9M - 1 electronic structure 1.1 wave model 1.2 valence bond molecular orbital 1E9M - Schrodinger equation (or dirac equation in relativistic quantum chemistry) reactive force fields, quantum chemistry, quantum field theory, 1E9M - Electronic molecular hamiltonian, born-oppenheimer approximation, determining the electronic structure of the molecule, 1E9M - Wave model, in which the atom is a small dense, positively charged nucleus surrounded by electrons,bohr model of the atom, describes electrons as "clouds" moving in orbitals, 1E9M - Probability distributions, discrete points, model predictive power, 1E9M - Predicts the pattern of chemically similar elements found in the periodic table, 1E9M - Pairwise interactions between atoms,the valence-bond (vb) [or heitler-london-slater-pauling (hlsp)] method, 1E9M - Method classical chemists' drawings of bonds, 1E9M - Mathematical functions delocalized over an entire molecule, hund-mulliken approach or molecular orbital (mo) method,capable of predicting spectroscopic properties, the thomas-fermi model, 1E9M - Describe many-electron systems on the basis of electronic density instead of wave functions, 1E9M - Density functional theory, polyatomic molecules and macromolecules, study the motion of molecules. 1E9M - Direct solution of the schrodinger equation, quantum molecular dynamics, 1E9M - Semiclassical approximation semiclassical molecular dynamics, 1E9M - Classical mechanics framework molecular dynamics (md), 1E9M - Statistical approaches, monte carlo methods, adiabatic chemical dynamics, 1E9M - Born-oppenheimer approximation, interatomic interactions are represented a single scalar potentials potential energy surfaces, 1E9M - Pioneering applications of, rrkm theory, marcus transition state theory developed by eyring, 1E9M - Methods simple estimates of unimolecular reaction rates, 1E9M - Characteristics of the potential surface, non adiabatic chemical dynamics, vibronic coupling, 1E9M - Different electronic quantum states of the molecule, landau-zener transition, transition probability between two diabatic potential curves 1E9M - Photomagneton, plasmas, basic quantization of the underlying bosonic field, 1E9M - Quantum hydrodynamics, de novo fragment-based approach, the identification of novel small molecule drug candidates, 1E9M - Chemistry and biology expertise, internal programs, new therapeutic modalities, 1E9M - High nanomolar inhibitor, 1E9M - Treatment of, low nanomolar ligand potency, drug targets, 1E9M - Docking a small molecule, 1E9M - Library screening, 1E9M - Normal mode analysis, 1E9M - Protein movements and conformational changes modeling and simulation, 1E9M - Mutagenesis, 1E9M - Qm-based solubility (water, dmso) prediction, 1E9M - Qm-based pka (protonation states) predictions, 1E9M - Ic50 of a protein-ligand complex, 1E9M - Description: calculates the free binding energy and predicts the ic50 of any protein-protein complex with known coordinates, 1E9M - Price, sources of 3d biological macromolecular structure data, 1E9M - Pdb format standard formats .hin, .mol2 etc. ligand flexible bonds, receive a .pdb file with coordinates of the 1E9M - Ic50 umol/l - ic50 value, 1E9M - E bind, kj/mol - free binding energy, 1E9M - E es, kj/mol - electrostatic and solvation energy, 1E9M - E vdw, kj/mol - short range electrostatic and exchange and van der waals energies, 1E9M - Tds, kj/mol - entropy contribution, 1E9M - E tor, kj/mol - ligand internal energy change, 1E9M - Charge, mass, flex.bonds - total charge, mass and number of flexible bonds of the ligand, 1E9M - Rmsd, a - root mean square distance between the initial and final positions, errors, 1E9M - Accuracy of the prediction, absolute deviation . 8 kj, deviation . 15%, proof of consept_ic50, 1E9M - Finds the position of a small molecule in the active site of a given protein, 1E9M - Minimum value of the free binding energy, 1E9M - Predicts the ic50 of the ligand, 1E9M - The ligand docking module, 1E9M - The position of the active site of, 1E9M - Coordinates (or number in the protein structure) of any atom near the center 1E9M - Of the active site, 1E9M - Find the position of the small molecules from a virtual library in the active site of a given protein, 1E9M - Synthetic compounds; diversified set of synthetic compounds, natural compounds; diversified set of natural compounds, 1E9M - Super-diversified set from collection of 500,000 compounds, 1E9M - Synthetic and natural scaffold compounds, 1E9M - Qm-based solubility (water, dmso) prediction, 1E9M - Calculate the solvation energy and solubility for a library of molecules, 1E9M - Number of solvents (water and dmso), . 1E9M - Solvation (g/l), 1E9M - Solvation energy (kcal/mol), 1E9M - Solubility (solvation) - the maximum quantity of solute that can dissolve in a certain quantity of solvent, solvation energy energy require 1E9M - Transfer a mole of a solute from a gas phase to solvent, 1E9M - Qm-based pka (protonation states) predictions, 1E9M - Analyzes a molecule, 1E9M - Finds protonation states, 1E9M - Calculates pka values for various protonation reactions, 1E9M - Identify the proper protonation state for a given ph, 1E9M - Molecule contain more than heavy atoms, 1E9M - All identified protonation states, 1E9M - Pka values corresponding to the dissociation reactions between the states, 1E9M - Single graph, containing the relative concentration for each of the protonation state of the molecule as a function of ph, 1E9M - Absolute deviation . 1 ph unit, proof of consept_protonation state, pka, 1E9M - Filtering of chemical libraries, enrich compound library, 1E9M - Alkaloids, steroids, flavonoids, coumarins, terpenoids, sesquiterpene lactones, 1E9M - Glycosides, peptides, purines,pyrimidines, antivirals, 1E9M - Antibacterials, tuberculostatics,anti-infectives, anti-inflammatory, agents, cancerostatics, antidiabetics, 1E9M - Cardiovascular, activity, hypo/hypertensives, neurotropic agents, cns regulators, 1E9M - Computer-aided, optimization, prediction,bio-effect, combinatorial chemistry, plant protection, 1E9M - Crop, combinatorial library, potential hits/leads, targeted sub-array,nearest analogs, 1E9M - Structural-topological characteristics, bioeffect, fungistatics, 1E9M - Antidiuretics, immunostimulants,parasitocides, antipyretics, psychostimulants, psychomimetics,antirheumatics, 1E9M - Tuberculostatics, antiulcer agents, virulicides, business development, 1E9M - Vendors,validation,virtual, 1E9M - Virtual library, 1E9M - Virtual screening, 1E9M - Protein-protein interactions,disease pathways, 1E9M - Target identification, 1E9M - De novo drug design, rational drug design, structure based drug design,media, press, release, latest, updates, last, today, 1E9M - Technology, chemoinformatics, lead discovery, drug development, pipeline, 1E9M - Health, healthcare, physics, contract services, applications, 1E9M - Quantitative structure-activity relationships, qsar, software, solutions, tool, 1E9M - Genomics, proteomics, biotechnology, docking, high-throughput screening, 1E9M - Computer-aided drug design, molecular biology, hts, farmacology, molecular design,pharmaceuticals, 1E9M - Drug discovery, 1E9M - Drug discovery company, 1E9M - Drug candidate, 1E9M - Lead drug, 1E9M - Lead optimization, 1E9M - Free binding energy, affinity, binding constant, ic50, affinity constant, 1E9M - Binding free energy, ab-initio calculations, entropy contribution, 1E9M - Van der waals, electrostatic, 1E9M - Flexible ligand, docking screening dock screen 1E9M - Flexible protein, docking screening dock screen 1E9M - Docking, first principles, 1E9M - Full flexibility of molecules, 1E9M - Solvation effects, 1E9M - Entropy contribution, 1E9M - Ab initio, small molecule, drugs, drug design, computational technology, 1E9M - Biotechnology, computational chemistry, bioinformatic techniques,complexity theory, 1E9M - Drug discovery platform, inhibitors, 1E9M - Ligand, 1E9M - Docking software, 1E9M - Software development, 1E9M - Drug discovery software, 1E9M - Scoring function, 1E9M - Force field, linear scaling, 1E9M - Molecular modeling, 1E9M - R&d, 1E9M - Computational technology, 1E9M - Target protein, novel molecule, design, algorithm, out-source, 1E9M - Platform, quantum computer, drug rescue, collaboration, partnership, 1E9M - Contract research, qsar, structure-based design, research and development, 1E9M - Quantitative structure-activity relationships in medicinal, agricultural, or environmental chemistry, 1E9M - De novo design, affinity calculations, 1E9M - Quantum calculations, free-energy calculations, 1E9M - Binding proteins, binding site, structure based design, molecular design, 1E9M - Collaborative services, assay development, hts, high-throughput screening, high throughput screening, 1E9M - Compound design, targeted, focused, screening libraries, compound libraries, 1E9M - Lead profiling, informatics, bioinformatics, full lead optimisation, 1E9M - Hit-to-lead, molecular informatics, 1E9M - Pharma, pharmaceuticals, pharmacology, 1E9M - Pharmacophore analysis, 1E9M - Receptor, validation, virtual, 1E9M - Virtual library, virtual screening, parallel, 1E9M - Consulting, contract, validation, verification, 1E9M - Evaluation, analysis, bioanalysis, assessment, 1E9M - Protein preparation, binding site analysis, collaboration, 1E9M - Partnership, investment, cost reduction, time to drug, start-up, event, news, achievement, prominent, outstanding, russia, european, mosco 1E9M - Leads 1E9M - Lead identification, 1E9M - High throughput screening, virtual screening, proteins, leads, 1E9M - Reduced rate of drug failure, clinical trials, new drugs, novel molecule, 1E9M - Intermolecular interactions, 1E9M - Lead identification, 1E9M - Lead optimization, moscow based, russian technology 1E9M - Computational technology platform, biotech companies, 1E9M - Articles,scientific activity, proprietary computational technology platform, 1E9M - 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Level of accuracy,computer.s power, screening the library,in silico, library,hit identification, 1E9M - Identification,seed structures,lead development, lead optimization, 1E9M - Constructs novel molecules,improved drug-like properties, 3d protein, 1E9M - Seed, built,expert, optimized leads,evaluation,synthesized, testing,tools, 1E9M - Binding energy calculated, entities, pre-defined proprieties, obtained, 1E9M - Optimization procedure, build new entities,improved properties, small-molecule drug candidates, 1E9M - Disease targets, target protein, quantum, qoptimal, qbuilder, complexity analysis of quantum systems, 1E9M - Calculation of binding free energy, docking, screening, lead optimization, protein-ligand complex, 1E9M - Genetic algorithms, 1E9M - Optimal lead configuration, 1E9M - Drug-likeness, 1E9M - Admet,adsorption, distribution, metabolism, excretion,toxicity, properties, quantum mechanics, 1E9M - Statistical physics, linear scaling, estimate binding affinity, condensed matter physics, 3d, protein structure, 1E9M - Protein flexibility, 1E9M - Accurate calculation of binding free energy, 1E9M - Hit identification, 1E9M - Seed structure, coordinates of the active site of the protein, biochemistry, quantum computer, protein folding, 1E9M - Linux supercluster, quantum pharmaceuticals, drug discovery,new, drugs, laboratory, lab, biochemists, 1E9M - Biophysicists, researchers, identify, nature of a disease 1E9M - Biological markers, proteins, drug, candidates, preclinical, 1E9M - Clinica, trials, graphic, drug development, process, target identification, 1E9M - Targets, disease, scientists, techniques, to identify and isolate a target, functions, 1E9M - Target prioritization, validation, biological, 1E9M - Chemical, interactions, molecules, lead, diseased cells, lead identification, 1E9M - Lead compound, substance, potential, treat, 1E9M - Identify lead compounds, chemicals,tested, collection,individual molecules, properties, 1E9M - Lead optimization, main,leads, discovered, 1E9M - Build new leads, optimized properties, safe, effective, medicines, 1E9M - Force fields, pipeline, dft, hartree-fock, protein folding, structure-based drug design, 1E9M - Flexible protein-ligand molecular 1E9M - Docking, protein flexibility, 1E9M - Protein ensembles, 1E9M - Ab-intio calculations, 1E9M - Protein-ligand complex, 1E9M - Drug discovery, pre-clinical, technology, development of a drug, laboratory tests, 1E9M - Effect, investigational drug, living organisms, in vivo,cells,test tube, in vitro,pharmacology, 1E9M - Toxicology, results,experts,formulate the drug, clinical, candidate drug, studies,risks to humans,identified, 1E9M - Quantum pharmaceuticals, drug discovery, pre-clinical, technology, development of a drug, laboratory tests, 1E9M - Effect, investigational drug, living organisms, in vivo,cells,test tube, in vitro,pharmacology,toxicology, 1E9M - Results,experts,formulate the drug, clinical, candidate drug, studies,risks to humans,identified, 1E9M - Phase i clinical studies, designed, verify, safety, tolerability,candidate, healthy,investigational drug,observation, 1E9M - Absorbed, distributed, metabolized, excreted, patients, target, disease, minimum,maximum, 1E9M - Effective, dose, development, approved, certified, ,complexity,theory,tool,platform,inhibitors,integrase,ligand, 1E9M - Novel drug candidates, drug targets, protein, pharmacokinetic,structure based drug design, 1E9M - Research,de-novo,innovative,biomed,life science, ools, quantum, pharmaceuticals, 1E9M - Drug discovery, computational, platform, structure based drug design, qoptimal, qbuilder, 1E9M - Basis, docking, screening, lead, optimization, technology, rapid,identify, novel, 1E9M - Drug-like, molecules, target,entirely, in silico, 1E9M - Proprietary, tool, developed, quantum mechanics, statistical physics, 1E9M - Methods, calculates, binding, free energy, protein-ligand complex 1E9M - Estimate, binding affinity, computational algorithms, linear scaling, 1E9M - Accuracy, calculations, systematically improved, fast,accurate, 1E9M - Global, minimum, searches, complex, systems, artificial intelligence, 1E9M - Genetic algorithms, docking procedure, lead optimization, 1E9M - Protein, ligand, active, binding site, free binding energy,optimization, 1E9M - Optimal lead configuration, active site of the protein, 1E9M - Proprietary tool,constructs, novel, molecular, entities,active site, 1E9M - Library,organic, fragments, entities, drug candidates, required, 1E9M - Binding affinities,drug-likeness,computational technology, methods, 1E9M - Based, first principles, physics, (ab initio),self consistent, model 1E9M - Intermolecular forces, molecules, in solutions,training set, adjustable parameters, 1E9M - Flexible ligands, flexible proteins, thermodynamic, 1E9M - Values,entropy,into account, lead optimization in silico, 1E9M - Revolutionary in drug discovery, advancement, scoring functions, 1E9M - 1E9M - Screening, large, libraries, chemical, linear scaling, compounds, latest versions, compute, 1E9M - Preparation, quantum chemical models, cubic scaling, 1E9M - Molecules, thousands of atoms,the accuracy and speed, 1E9M - Computer applications, blocks, scientific, quantum, proprietary tool, 1E9M - Quantum mechanics,statistical physics, methods,calculates, binding free energy, 1E9M - Protein-ligand complex, binding affinity, computational algorithms, linear scaling,accuracy, 1E9M - Complexity analysis,quantum systems, condensed matter physics, first principles of physics, 1E9M - Factors,binding free energy,electrostatic contribution, van der waals energy, 1E9M - Hydrophobic interactions, entropic free energy contribution, competitive advantage, 1E9M - Fitting parameters, quantum physics, protein flexibility,binding sites, non-rigid, entities, 1E9M - Time-effective, precision, calculations, the tools, techniques of drug discovery, bioinformatics, computational biology, 1E9M - Computational chemistry, biotech, rational drug design, in-silico technologies, software, newly, modern, 1E9M - Complexity analysis, calculation,interaction, molecules, methods, quantum physics, 1E9M - Scales, exponentially, number of atoms, modern, computer, advanced algorithms, 1E9M - Supercomputer, solve for a molecule consisting of 1000 or more atoms, 1E9M - Accuracy,approximate, empirical, methods, optimal, quantum information, 1E9M - Complexity theory analysis, molecular,description of the molecular structure, 1E9M - Information capacity, interacting electrons, atoms, three-dimensional, 1E9M - Molecule interactions, scientific group, quantum calculation, polynomial, 1E9M - Empirical methods, scoring functions, force fields, application, 1E9M - Quantum methods, dft, hartree-fock, computer, aided, drug, discovery, 1E9M - Technology, assay development, library management, primary sreening, secondary screening, 1E9M - Generate and screen new patentable molecules against their targets, 1E9M - Discovery of novel, patentable leads, proprietary chemistries, 1E9M - Pharmacogenetic, minimum-search algorithm, structure generation, virtual screening, 1E9M - Library design, focused chemical library, 1E9M - Targeted, virtual library, de novo,novel, 1E9M - Chemical structure generation, molecular similarity, 1E9M - Ligand conformation, biomolecular, 1E9M - Hit expansion, structure based, drug design, 1E9M - Pharmaceuticals,qauntum,ligand, inhibitor, docking, virtual docking, protein, target, 1E9M - Screening, virtual screening, library, against the protein, lead optimization, 1E9M - Ligand docking, minimum, binding energy, 1E9M - Protein-ligand complex,3-d protein, structure,active site,data, 1E9M - Docked ligand, binding free energy, calculates, binding, energy, 1E9M - Optimization, docking, experimental, simulation,molecular, qsar, 1E9M - Screening the library, in silico, hit, identification, 1E9M - Focused library,seed,lead development, compound, novel molecules, 1E9M - Improved, drug-like, properties, seed,optimized leads, 1E9M - Synthesized,structures,entities, services, outsourcing, 1E9M - Out-sourcing, cro, contract research, 1E9M - Ligand docking, ligand, docking,protein, minimum, binding, energy, 1E9M - Protein-ligand complex, input, data, 3-d protein structure, 1E9M - Ligand structure, coordinates, active site,output,docked ligand, 1E9M - Binding free energy, blocks, quantum, calculates, de nove drug design, 1E9M - Binding, energy, optimization procedures,complex, drug discovery, 1E9M - Early, in-silico, software, computational, rational drug design, de-novo drug design, 1E9M - Novel drug, lead optimization, lead, leads, ligands, inhibitor, inhibition, ic50, inhibition constant, 1E9M - Affinity constant, binding affinity, screening, library,in silico, 1E9M - Minimum, binding free energy,ligand, docking, hit, 1E9M - Identification, focused libraries, protein, 1E9M - Identification, lead, seed, .seed structures., 1E9M - Lead development, million, compounds,accuracy, 1E9M - Power, computer,rational drug design, drug discovery, 1E9M - De-novo drug discovery, novel, drug, pipeline, lead optimization, 1E9M - Technological, process, quantum pharmaceuticals,constructs, novel, 1E9M - Molecules, improved, drug-like, properties,input, data, 3d protein, structure, 1E9M - Seed, ligand, structures, coordinates,active site, protein,expert,screening, library, 1E9M - Optimized,leads, evaluation,synthesized, testing,binding energy calculated, 1E9M - Quantum, seed,entities, optimization, science, technology, 1E9M - Drug discovery,business, strategy, quantum, small, research, 1E9M - Project,pkd, values, computed, docking, docking programs, technology, complexes, 1E9M - Evaluation, results,comparison, file, experimental pkd, calculated,figures,data, 1E9M - Accuracy,advantage,docking, 1E9M - Programs,structure based drug design,advancement, scoring functions, 1E9M - Empirical, approximation, pki, docking, rational drug design, web, internet, 1E9M - Interface, demonstration, computational technology, 1E9M - Quantum pharmaceuticals, biotech, pharmaceuticals, community,test, 1E9M - Docking program,information,results,3d, protein, structure,pdb,code, 1E9M - Ligand,hin, format,atom,active site,protein,atoms,calculations, 1E9M - Optimal coordinates,minimum, pkd, free binding energy,calculations, 1E9M - Perform,business,website, 1E9M - Quantum 3.1,ligand file, indicate, active site, screening techologies,pharmaceutical industry,targets, 1E9M - Advances, genomics, mapping, human genome,proteins, investigation, 1E9M - R&d,identify, high quality, lead, candidates,reduced failure rates, lead identification,wet, 1E9M - Chemistry,combinatorial chemistry, 1E9M - High-throughput screening, hts,ultra high throughput screening, uhts,test,binding affinity,high-throughput,screening, 1E9M - Compounds, 1E9M - Laboratory, binding activity,biological, activity, molecules,identification of leads, 1E9M - Random screening,library,design, approach, 1E9M - Rational, analogs,drug,active, target receptor,researchers,compound collections,searching,assays, 1E9M - Hit, assaying, facilities, 1E9M - Pharmaceutical companies, lead identification,approximate,technical, problems, 1E9M - False-positives,negatives,promiscuous,non-drug-like, 1E9M - Degradation of compounds,screening plates, limited compound purity, 1E9M - Concentrations, inconsistent plate replication, evaporation, 1E9M - Hit rates,receptors,collections,synthesized compounds, natural products,chemical diversity, 1E9M - Smart screening,pre-focus, 1E9M - Optimize properties,marketable drugs,newly identified targets, 1E9M - Computational,genome sequence,3d structure, protein function, 1E9M - Lead compound, computer, in silico, virtual screening, vs, provided, 1E9M - Solutions,methods, designed, compound databases, candidate, molecules, 1E9M - Novel, chemical, entities,biological activity, focused,computational analysis, 1E9M - Subset of compounds, virtual library, molecular structures, 1E9M - Filtered,small,experimental, biological assay, molecular weight, limitations, 1E9M - Drug, false positives,false negatives, 1E9M - Calibration, scoring functions,experiment, scoring method,binding affinity,novel structures, 1E9M - Molecular fragment, position, 1E9M - Receptor pocket,prioritized, score, quantum computer, developing, methods, algorithms, 1E9M - Biochemistry, science, technology, scientific,expert, devices, simulate,principles,computational resources, 1E9M - Solutions,complex systems, exponential scaling, polynomial time,protein folding,lead discovery, 1E9M - Optimization,resolving,3-d structure,computational technology, x-ray spectroscopy, model, research, 1E9M - Local minimum energy, conformations, evaluate, molecule, drug properties,chemical,contract service, 1E9M - Contract services, molecules, drug candidates, drug industry, 1E9M - Genetic, neural network, quantum computer, works, quantum mechanics, effect, schrodinger, experiment, 1E9M - Drug discovery, technology, news, events, experiment, simultaneously,superposition, device, computes, 1E9M - Bits, qubits, configurations,physically, exponentially, operations, computational, mathematical, numbers, 1E9M - Computer, computation, parallel, computational resources, new, small-molecule, drug candidates, 1E9M - Cost of drug discovery, cost, drug discovery process, steps in drug development, drug development, 1E9M - Target identification, target validation, target prioritization, business development models, 1E9M - Participation in governmental and non-profit initiatives, drug discovery program, offer, 1E9M - Biotech, pharmaceutical companies, product, developed, collaboration, interbioscreen, collection, 1E9M - Q-lead-libraries, q-lead-library,library of compounds, ranked, constant affinity,protein, disease, 1E9M - Target,molecules, 1E9M - Top,list, highest, affinity, hits, drug optimization, diseases, natural, synthetic, compounds 1E9M - Bioactivity,pmol, nmol, mkmol, target protein,major, russian, research, centers, physico-chemical biology , 1E9M - Expertise,researchers, research laboratories, 1E9M - Products, services, quantumlead, web site, q-lead, r&d, program,develop, drugs,areas, 1E9M - In-house, collaborations, 1E9M - Replication, cycle, integration, lead compounds,structure based design,identify, novel lead compounds, 1E9M - Binding affinities, 1E9M - 10-8 mol/l, drug-likeness, properties, propriatory, technology,leads, scaffolds, 1E9M - Developing, novel, drug candidates, 1E9M - Invasion, leads, penetrate, extracellular matrix, scientists, folding, cellular proteins, receptors, 1E9M - 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Drug discovery technology, drug-like, hit generation, htos, lead discovery, lead generation, minimum-search algorithm, 1E9M - Structure generation, library design, focused chemical library, virtual library, de novo chemical structure generation, 1E9M - Molecular similarity, ligand conformation, biomolecular, hit expansion, early stage, medicinal chemistry, 1E9M - Lead licensing, drug candidate licensing, assay development, library management, primary sreening, 1E9M - Secondary screening, computational simulation,integrated, outsourcing, services,synthesis, virtual screening, 1E9M - In-vitro,testing, collaboration,facilities, in silico, lead, optimization, technology, in-house program, 1E9M - Pharmacological activity, collaborative, generation, collection, synthetic, natural, compound, libraries, 1E9M - Chemists, russia,hit, rich, libraries,protein, targets, defined, binding, free, energy, q-lead-libraries, 1E9M - Hits, leads,drug candidates, disease-protein,synthesis,development, new, chemical, drug-like,enhanced, 1E9M - Collaborations, major,research, protein, target, inhibitor, ihnibition, constant,biochemistry,physico-chemical 1E9M - , biology, provider, screening, international, discovery, application, commercialize,focus,industry,business,technology, 1E9M - Physico-chemical property calculations, drug-like characteristic selection parameters, 1E9M - Prediction, purchasing, compound acquisition, drug discovery,chemical compound supplier, 1E9M - High throughput screening,combinatorial,libraries,hts,organic chemistry suppliers, 1E9M - Small molecule leads, validated disease targets, generate and screen new patentable molecules against their targets, 1E9M - Discovery of novel, patentable leads, proprietary chemistries, pharmacogenetic, profile, pdb, protein data, directory, list, 1E9M - Conference, applied, approach, first principles,denovo,supercomputer, 1E9M - Screening, custom synthesis, pharmaceutical, lead optimization, virtual docking, 1E9M - Contract reseach,cheminformatics, virtual screening techniques, 1E9M - Diverse focused compound libraries, substance, prescreened libraries, targeted library, 1E9M - Collection, novel, preferred, templates, assay, 1E9M - Lead discovery, drug-like focused libraries,advanced combinatorial libraries,adme profiling, 1E9M - Biotech, analog synthesis, research and development, agricultural,toxicity,lead generation, 1E9M - Organic compounds, cluster,analysis,biologically, active,chemical, compounds,human, health,structure, 1E9M - Modelling, biochemical, medicine,pharmacology,biosystems,protein kinase inhibitors, anticancer compound, 1E9M - Cro, outsourcing, out-sourcing,custom synthesis, supply, preparation, diversified, virtual,focused,targeted, 1E9M - Library, synthetic, compounds, natural, elite, drug, like,lead,virtual screening, quantum, 1E9M - Free binding energy, protein-ligand complex,algorithm, based,ab initio, methods, quantum,statistical, 1E9M - Physicsl,composition, 1E9M - Hit, analysis,developing,analog, derivative, set,experimental testing,targeted,q-lead-library, 1E9M - Binding affinity, hit optimization, 1E9M - Combination, calculations,entities,bioactivity, accuracy,affinity constant,assays,ligand,service, 1E9M - Solution, in-vitro, in-vivo, 1E9M - Technology,products, portfolio, chemistry tools, small molecule, drug discovery,discovery chemistry,advanced combinatorial library, 1E9M - Combinatorial, building blocks, diverse, compound collections, high-throughput screening,hts, uhts, 1E9M - Vendors,validation,virtual,virtual library,virtual screening, protein-protein interactions, disease pathways, 1E9M - Target identification, 1E9M - Related articles, comparative, evaluation, molecular docking, department, internal, medicine, comprehensive, 1E9M - Center, university, medical school, medicinal chemistry, college of pharmacy, medical center. scoring, functions, 1E9M - Tested,100, protein-ligand complexes, evaluate, 1E9M - Abilities, reproduce, experimentally, determined, structures, binding affinities, scoring functions implemented, 1E9M - Conformational, sampling, exhaustive conformational 1E9M - Sampling, program,generate, ensemble,docked conformations, conformational, required,conformational space, focus, 1E9M - Energy minima,applied, score,conformational ensemble,experimentally observed, decoys, yield, success rates, higher, 1E9M - Six, 66,6, root-mean-square, deviation, criterion, two, three, consensus, scoring scheme, improves, improved, 1E9M - Reproduce, experimentally determined binding affinities, protein-ligand complexes, correlation coefficients, 1E9M - Inspected, abilities, construct, descriptive, funnel-shaped, energy surface, protein-ligand complexation, 1E9M - Results, indicate,perform, better, aspect,introduction, today.s, flexible, docking, predict protein-ligand complex, 1E9M - Structures, reasonable, accuracy,speed,applications, virtual database, screening, approaches, hundreds, thousands, 1E9M - Docked, binding pocket,identify, plausible binders,used, prior, experimental, screening, powerful, computational,filters, 1E9M - Reduce labor and cost, dramatic, increase, number,druggable, biological targets,postgenomic era, conformational sampling, 1E9M - Procedure, docked conformations, explored, 1E9M - Genetic algorithm, monte carlo simulation, simulated annealing, distance geometry, miscellaneous methods, method is applied, 1E9M - Guided, energy function, fitness final accuracy of the scoring 1E9M - Function impact quality widely spread concept weaknessconsiderable development 1E9M - Computational methods describing protein ligand 1E9M - Interactions. past decade, number 1E9M - Grouped categories: force field methods, empirical scoring functions, knowledge-based 1E9M - Potentials.validated on various sets comparative studies of various scoring 1E9M - Functions selected targets. judged by docking accuracy, scoring accuracy, 1E9M - Ability to identify known active compounds 1E9M - From a random pool docking/scoring combination 1E9M - Reliably valid approach 1E9M - Seeking active compounds 1E9M - Virtual database screening 1E9M - Performance complicated drawback emphasize 1E9M - Procedure docking algorithm fails, .default. set of parameters, guarantee 1E9M - Adequate sampling possible docked conformations. 1E9M - Biased invalid. ideally explore protein-ligand interactions dominated by hydrophobic factors 1E9M - Various settings parameters controlling conformational sampling, fair evaluation 1E9M - Isolate conformational sampling procedure ground. ensemble diversity energy minima 1E9M - Spectrum performance 913 reproduces experimentally 1E9M - Determined structures constructs a descriptive, funnel-shaped energy 1E9M - Surface for protein-ligand complexation. strength weakness consensus scoring, practical strategy 1E9M - Docking accuracy, methods preparation 1E9M - Test set, crystal structures, experimentally measured ki, kd values resolution 1E9M - Better . molecular weights ligand molecules range from to rotatable single 1E9M - Bonds (rotors) dissociation constants complexes (in -log kd or -log ki units), spanning orders of 1E9M - Magnitudes, noncovalently, coordinates, computation,split 1E9M - Metal ions, residing, organic and inorganic 1E9M - Cofactors, water molecules, removed.hydrogen atoms atom types and bond types corrected charges. 1E9M - Version graphics workstation. conformational sampling procedure. genetic algorithm (ga) run outputs 1E9M - A population chromosomes, crossover ratio mutation ratio elitism ratio rotatable single bonds in the ligand, i.e., sp3- 1E9M - Sp3 and sp3-sp2, are allowed to rotate rotations different conformations, sconnecting a terminal -ch3 group. flexibility in cyclic 1E9M - Parts neglected. searching steps for translation, torsions a, the size of the docking box, experimentally observed position, 1E9M - Binding pocket observed, grid spacing largest 1E9M - Docking box initial conformations randomly miscellaneous parameters assigned default values 1E9M - Fixed subsequent scoring function evaluations, depict 1E9M - Conformational space focus on a few fully integrated drug discovery programmes 1E9M - Hit-to-lead cadd energy minima favored root-mean-square deviation (rmsd) 1E9M - Values (calculated distinctive conformational clusters clustering criterion diversity of the 1E9M - Ensemble.proper sampling global minimum pdb resoln description 1E9M - Knowledge-based potentials of mean force, i.e., pmf and drugscore. parameter/options 1E9M - Multi-mol2 file. spreadsheet valid input for computation. translated into sdf babel program 1E9M - Computations perl script compile them into one table. indicates a higher binding affinity. 1E9M - Commercially available original authors many researchers in this 1E9M - Closely the best-scored (or the lowest-energy) predicted 1E9M - Experimental complex structure. best scored 1E9M - Default criterion tighter 1E9M - Criterion looser criterion. rankings scoring functions 1E9M - Nonduplicate conformations is taken into account. 1E9M - Appear output multiple docked conformations for 1E9M - Analysis.subsets according chemical nature classification aided 1E9M - Contribution of the h-bond term hydrophobic term, hydrophilic mixed factors summarized 1E9M - Hydrophobic subset,different rmsd criteria 1E9M - Success rate (%) scoring functiona 1E9M - Rmsd 1E9M - Multiple conformations 1E9M - Success rate (%) when considering scoring function 1E9M - Only the best conformation 1E9M - The best two conformations 1E9M - The best three conformations 1E9M - Nonspecific and nondirectional characterized. 1E9M - Well-balanced considerations of polar and nonpolar, enthalpic and entropic 1E9M - Factors in protein-ligand binding calibrated inferior performance simple distance and angular 1E9M - Functions equations, chemical intuition statistical analysis of 1E9M - A large number of experimental structures. atomic 1E9M - Radii independently derived.knowledge-based potential 1E9M - Mean force approach, interpreting 1E9M - Inverse boltzmann distributions equation combining pairwise potentials 1E9M - And molecular surface based potentials.hydrophobic effect 1E9M - Distance-dependent pairwise potentials. pairwise potentials 1E9M - Muggue.s pmf approach performs mixed subsets brute force 1E9M - Describing intermolecular interactions. 1E9M - Truncating the noncovalent part of a force 1E9M - Field special reparametrization, adequately formularized compute solvation energy, extensive molecular dynamic samplings 1E9M - Electrostatic interaction energy. atom-centered partial charges theoretical derivation 1E9M - Solvent state-of-the-art atomic charges dielectric constant. bulk solvent, 1E9M - Electrostatic microenvironment distancedependent 1E9M - Dielectric constant compute the electrostatic 1E9M - Interactions unit-atom charges for proteins, distance-dependent dielectric constant computation. 1E9M - Scheme bound conformation of a given ligand from 1E9M - Computer-generated decoys. double and triple combinations 1E9M - Rank-by-rank. strategy candidates bestranked 1E9M - Conformation level of success rates outperform single 1E9M - Scoring repeated measurements reduce noise data collection 1E9M - Converged effectiveness obtaining blind combination 1E9M - Arbitrary scoring functions binding affinity prediction. practical application, virtual 1E9M - Database screening, binding scores. predict real binding affinities. 1E9M - Correlations scores and experimentally measured binding affinities linear. spearman correlation coefficient 1E9M - Correlation between two sets of rankings, is a proper quantitative measurement 1E9M - Equations complementary computed corresponds inverse correlation, total disorder.experimental structure. summarized 1E9M - Best agreement between its scores and the experimental 1E9M - Binding affinities with a correlation coefficient scoreaffinity 1E9M - Correlations score-affinity correlations. (kcal/mol) score-affinity correlation 1E9M - Scoring function developers 1E9M - Funnel-shaped energy surface of proteinligand 1E9M - Complexation, funnelshaped 1E9M - Energy surface receptorligand 1E9M - Complexation initial position, binding pocket on the receptor bind correct location of the global minimum, 1E9M - Descriptive funnel-shaped energy surface false minima funnel bottom 1E9M - Rmsd-score correlation multidimensional energy surface. quantitative measurement. 1E9M - Rmsd-score correlation outliers, chloramphenicol 1E9M - Chloramphenicol acetyltransferases h-bonding groups hydroxyl 1E9M - Groups, amide group, nitro group, failures removal crystal 1E9M - Complex structure, hole alternative binding pocket. water-mediated protein-ligand 1E9M - Placing discrete water molecules shallow 1E9M - Groove well-defined pocket specific interactions moderate 1E9M - Protein-ligand binding affinity (-log kd ) chloramphenicol acetyltransferase in 1E9M - Complex with chloramphenicol ball-and-stick model. possible h-bonds. groove overlap identify a specific binding area. 1E9M - Sum of intermolecular interactions between the complex 1E9M - Internal steric energy of the ligand. 1E9M - Vacuom force field lennard-jones dispersion-repulsion term, 1E9M - Directional hydrogen bonding term, where e(t) is an angular 1E9M - Weight factor, coulombic electrostatic potential. 1E9M - Vdw is a softened lennard-jones potential, 1E9M - C+pol buried polar surface area between 1E9M - The square of the buried polar surface 1E9M - Area between the complex involving both attractive and 1E9M - Repulsive protein-ligand interactions. exact 1E9M - Sum of pairwise linear potentials between ligand 1E9M - Protein heavy atoms with parameters dependent 1E9M - Interaction type. hydrogen bond donors, acceptors, donor/acceptors, or 1E9M - Nonpolar. hydrogenbonding between donors and acceptors, repulsive donordonor 1E9M - Acceptor-acceptor contacts, and generic dispersion of other contacts. hydrogen bonding 1E9M - Repulsive terms are modulated by a scaling factor 1E9M - Crude distance and angular dependence. 1E9M - Small (fluorine and metal ion), medium (carbon, oxygen, 1E9M - And nitrogen), and large (sulfur, phosphorus, chlorine, 1E9M - And bromine) atoms are assigned atomic 1E9M - Radii parameters interatomic distances high-quality crystal structures. 1E9M - Statistical sense. mean force (pmf) 1E9M - Scoring function muegge distance-dependent interaction potentials for 1E9M - Various atom pairs. enthalpic and entropic effects 1E9M - Distance cutoff carbon-carbon interactions 1E9M - Report pioneering dissects protein-ligand 1E9M - Binding free energy as edock ) evdw + eh-bond + eelectrostatic + einternal 1E9M - Eh-bond + erepulsion + econtact 1E9M - Pmf ) neutral. and.ionic. hydrogen bonds treated separately. scaled 1E9M - Distance- and angle-dependent function penalize the deviations from an ideal geometry. 1E9M - Buried hydrophobic molecular surface. 1E9M - Rotatable single bonds(rotors) in the ligand, torsional entropy loss of the ligand regression 1E9M - Constant. calibrated by fitting 1E9M - Known dissociation constants weight factors fitting 1E9M - Outperforms interactions between aromatic groups on both sides, 1E9M - Scaled distance- and angle-dependent function. general distance-dependent 1E9M - Potential for protein-ligand atom contacts. standard rotor term accounting for torsional 1E9M - Entropy loss reproducing the three-dimensional structures 1E9M - Complexation term, a hydrogen bonding term, 1E9M - And an internal energy term. reparametrized lennard-jones 8-4 potential. the hydrogen 1E9M - Bonding term sum of the individual energies 1E9M - All the donor-acceptor pairs complex.type and the 1E9M - Geometry of the donor-acceptor pair. internal 1E9M - Energy dispersion-repulsion energy torsional energy, sums van der waals 1E9M - Electrostatic interactions between the complex: 1E9M - Van der waals energy is calculated electrostatic energy is calculated with the coulombic equation. 1E9M - The distance-dependent dielectric constant neutral and ionic hydrogen 1E9M - Bonds metal ions residing inside the protein binding 1E9M - Pocket. hydrophobic effect, which is calculated by summing a distancedependent potential of all the hydrophobic atom pairs 1E9M - Formed between the complex. counts rotors, 1E9M - Contribution of each rotor is scaled solvent-accessible surface (sas) dependent singlet potentials for protein 1E9M - Ligand atoms: adjustable weight factor, pair-surface combination binding affinity estimation, 1E9M - Preliminary studies. number of .effective. rotors in the ligand molecule. calculates the 1E9M - Buried hydrophobic molecular surface of the ligand pairwise hydrophobic atom contact 1E9M - Potential microscopic match of hydrophobic ligand atoms to the binding 1E9M - Pocket relevant literature search strategies for automated molecular docking of flexible molecule databases 1E9M - Automated docking using a lamarckian genetic algorithm 1E9M - Empirical binding free energy function 1E9M - Fast flexible docking method 1E9M - Incremental construction algorithm. 1E9M - Development and validation of a genetic algorithm for flexible docking. 1E9M - Consensus scoring: empirical scoring functions 1E9M - The development of a fast empirical scoring function to estimate the binding affinity of 1E9M - Ligands in receptor complexes 1E9M - Molecular recognition of the inhibitor by 1E9M - Conformationally flexible docking 1E9M - Rational drug design: novel methodology and practical applications 1E9M - Fast method for the polarization of hits obtained from de novo 1E9M - Design or 3d database search programs. 1E9M - Development and validation of empirical scoring functions for structure-based binding 1E9M - Affinity prediction. 1E9M - A simplified potential approach. 1E9M - A knowledge-based scoring function for proteinligand 1E9M - Interactions: 1E9M - Probing the reference state. 1E9M - Effect of ligand volume correction on scoring. 1E9M - Protein-based virtual screening of chemical databases. 1E9M - Evaluation of different docking/scoring combinations. 1E9M - Detailed analysis of scoring functions for virtual screening. 1E9M - Concept for multidimensional selection of ligand 1E9M - Conformations 1E9M - Multidimensional scoring. 1E9M - A new program for the consensus analysis of protein-ligand interactions a method for obtaining improved hit rates 1E9M - From docking databases of three-dimensional structures into proteins 1E9M - An idealized computer experiment. 1E9M - Protein folding: the free energy surface. placing discrete water molecules during protein-ligand docking 1E9M - Predictions. 1E9M - A new force field for 1E9M - Molecular mechanical simulation of nucleic acids and proteins. 1E9M - Related fields, terms and keywords: 1E9M - Calculation of the ki for competitive and noncompetitive inhibitors, 1E9M - Designing a ligand - a potential drug candidate - which will interact specifically with a selected molecular target, 1E9M - Predict in-vitro estimation determinate lab bound small molecules faciliate modeling molecular 1E9M - Modelling camm cadd determination asisted computer assisted aided drug design 1E9M - Rational structure based prediction estimate binds 3d models coordinates measure 1E9M - In-silico mechanisms advances inhibits inhibited bio biochem computational altered predicted 1E9M - Values properties calculated appropriate scope set metabolism signal toxic end points computing 1E9M - Blocking docked virtual screening inhibiting native natural computational drug discovery technology 1E9M - Automated limit automatic machinery predictive powers simulation simulator accuracy dissosiation constant 1E9M - Ligand docking, performance kd perform relative selectivity associated confirmed yielded 1E9M - Nanomolar correlation known experimental comparison binding constant protein-ligand complexes 1E9M - Proof of concept average absolute error kj/mol; relative error rmsd applications technology developers. 1E9M - Platform range outstanding pkd molar dissolution dissociation constant pk receptor ab-initio first principals 1E9M - Chemoinformatics sar and pharmacological studies multigrid methods with local optimization 1E9M - Normal mode analyzer for identification of low energy temperature nmol entropy contribution 1E9M - Discativate limited cytotoxicity, neurotoxicity, accute or chronic toxicity linear scaling 1E9M - Quantum mechanics quantitative structure/activity relationship, receptor are scored, hierarchical filter, 1E9M - Genetic algorithm for protein-ligand docking, 3d-qsar technique, qm/mm, structure-based rational drug design, 1E9M - Knowledge based, rule-based expert system that predicts the toxicological hazard of chemicals, 1E9M - Adme characteristic predictions of drug candidates discovery informatics, solutions for computational chemists, 1E9M - Computational chemistry software, high-throuput virtual screening, high throughput discovery, ligand receptor docking, 1E9M - Framework consisting of a network of atoms with interconnecting bonds ligand-receptor binding free energies, analyser, calculator, 1E9M - Estimator, molecular analysis, 3d molecular model building software, predictions of pka, logp, logd values and metabolites, 1E9M - Computational methods van der waals, van der waals, web based, molecular simulations, computational out-sourcing, molecular design, 1E9M - Lead profiling, full lead optimisation, hit-to-lead, contract research services, full lead optimisation, optimization, 1E9M - Hit generation, htos, pka, lc-ms,lead discovery, lead generation, lead profiling, lead optimisation, drug discovery tool, 1E9M - Drug discovery platform, novel drug candidates, peptide, structure based drug design, research, de-novo, force fields, pipeline, 1E9M - Dft, hartree-fock, proprietary computational technology, quantum methods, cutting-edge technology, build new leads, 1E9M - Proprietary tools for structure based drug design, computer application tool, the accurate calculation of binding free energy, 1E9M - In-house, tools for the docking, screening, and lead optimization procedures, protein-ligand complex, computational algorithms, 1E9M - Drug development, linux cluster as a c++ program, parameters of intermolecular interactions, 1E9M - New small-molecule drug candidates for, hydrophobic interactions, and entropic free energy contribution, 1E9M - "large" molecules, minimum binding energy, the ligand structure, and the coordinates of the active site of the protein. 1E9M - The output data given are the coordinates of the docked ligand and the minimum value of the binding free energy, coordinates, 1E9M - Adme, admet, x-ray spectroscopy to model the 3-d structures of the majority of, cost, human encoded, binding affinities, 1E9M - Less, mol/l, preclinical and clinical trials, 1E9M - Target identification, 1E9M - Conformations, structural confromational changes, molecular computational model, mutations, structure, flexibility, 1E9M - Normal mode analysis, bioinformatics, structural research and analysis, domain motions, binding site, protein-protein interactions, 1E9M - Active site, complex, pka, optimization, optimisation, calculations, modelling, molecular computational model, discovery, 1E9M - Modeling interactions, biological activity, bioactivity, measurement, estimation, prediction, function protein movements, 1E9M - Mutated, case studies, disease target, toxic, admet, protein dynamics, superposition of collective variables, computer, 1E9M - Studies qsar study, computational, normal mode coordinates, desriptors, assessment, low-frequency normal modes, 1E9M - Degrees of freedom, geometry refinement (optimization),investigation, computation of lowest-frequency modes of, 1E9M - Conformational flexibility, pharmacophore, three-dimensional quantitative structure activity relationship methods, 1E9M - Conformational analysis, entropy losses, restriction of movements, simulate biochemical processes, anti , biologics, 1E9M - Simulation, inhibitors, ligands, blockator, molecular alignment models, pharmacophoric perception, homolog, homology, 1E9M - Structural basis for biological activity, modification changes, curve, landscape, finding sequences, 1E9M - Macromolecular structure determination and subsequent protein modeling, variable, biotech products, 1E9M - Dynamics structure, dynamic, molecular structural formula, crosslinking, energetics, charges, 1E9M - Id target identification, target validation, modelling protein modeling, model of atoms, 1E9M - Structural and functional similarity between, algorithm pharma bioanalysis, analytical, empirical, computational biology, 1E9M - Bioinformatics, biological activity of, mechanism, molecular dynamics (md), atomistic simulation, 1E9M - Neutralizing, molecular surfaces animations, view, drawings, micrographs and movies, presentation, 1E9M - Computer visualizations of, molecular dynamics, atom point mass, force rules describe, 1E9M - Newton's equations, to advance the atomic positions & velocities, thermodynamic statistics, 1E9M - Motion of the atoms, parallel algorithms that are useful for md simulations, variety of systems (atomic, polymer, biomolecular), 1E9M - Parallel platforms, short-range md force fields, atom-, force-, and spatial-decomposition algorithms, subset of atoms, 1E9M - Pairwise force computations proc, e simulation box, mechanism of association and dissociation of, 1E9M - Compute intra-molecular forces - e.g. bond, angle, torsional terms within molecule topology, 1E9M - Atom method, molecular-dynamics simulation of macromolecular systems, of substrates of enzyme reactions, 1E9M - External forces which reduce the energy barriers, electrochemical potential (proton motive force), 1E9M - Rotation leads to cyclic conformational changes, catalytic sites, identify and explore the chain of the elementary chemical 1E9M - (proton transfer) and mechanical (domain motion), converting the electrochemical energy, transmembrane proton, gradient, mechanical energy, 1E9M - Macromolecular systems, nma calculates vibrational normal modes, the lowest frequencies, describe the largest movements in a protein, 1E9M - Functionally relevant in terms of bioactivity, computed, explore the total conformational changes of, 1E9M - Compute modes for the whole protein, calculate modes for the active site, missing amino acid inside of the residue sequence, 1E9M - Several of the most vibrational modes and their animation, if the active site, indicate the central atom of the active site, 1E9M - Mutagenesis, compare the binding activity 1E9M - (ic50) for a protein and its mutated form regarding a known ligand, the 1E9M - 2d or 3d structure of a ligand, coordinates of the docked ligands to 1E9M - Native and mutated structures, corresponded affinity constants, 1E9M - Indicate amino acids of the native structure and their substitutions, 1E9M - Coordinates (or number in the protein structure) of any atom near the center of the active site, 1E9M - Comments, opinion, 3-d pharmacophores, 3d protein structure, computationally, identifying novel high affinity drug leads, 1E9M - Binding site, function for the protein, confirm and refine the protein structure, computational analysis, heavy atoms, 1E9M - Hydrogen atoms, proper protonation states assigned, exploring the conformation states of key residue side chains, 1E9M - Refined protein structure, modeling protein flexibility, the structure obtained from x-ray crystallography, homology modeling, 1E9M - Conformation on various time scales, potential binding sites conformations, clustered conformations, 1E9M - Fragment selection, primary fragment set, specific targe, produce leads, accurately predict experimental binding affinity, 1E9M - Empirical scoring approaches, binding site determination, identify small molecule binding sites on the protein surface, 1E9M - Binding site map, multi-dimensional analysis of fragment interactions, characterize the protein surface, 1E9M - Identify the key fragment interactions important for high affinity binding, mapping of the protein surface, 1E9M - Modeling the flexible protein-ligand complex, potential ligand is identified, the mechanism and dynamics of binding is studied, 1E9M - Differentiate candidate ligands, static and moving pictures of the protein-ligand complex, 1E9M - Binding energies equilibrated structures, isolated proteins, the nature of the binding, assemble molecules, innovative, 1E9M - De novo design system, free-energy information, binding site analysis, construct novel, patentable, 1E9M - High affinity compounds from the selected fragment set, 1E9M - Our methods allow chemists to tailor the building process toward desired physical properties, 1E9M - And chemistries amenable to synthesis, high success rate, 1E9M - Lead generation & optimization, the series of high affinity compounds, 1E9M - De novo design process, refined to identify a small set of drug leads, filtering process, 1E9M - Computational analysis of 1E9M - The result is a high quality lead series ready for pre-clinical development, 1E9M - Rapid generation of inhibitors and novel drug candidates, discovery and development of novel small molecules, 1E9M - Similar fragment-based access to de novo drug candidates, accurate energy calculations, computational methods, 1E9M - Approximate scoring 1E9M - Intermolecular forces predict energy calculate 1E9M - 1E9M - Focused library 1E9M - Focused compound library, targeted chemical collection, pre-selected, 1E9M - Prescreened, measurement, estimation, prediction, hts, 1E9M - Uhts, high throughput screening, ultra high-throughput screening, development, profiling, hit, 1E9M - Lead, hits, leads, drug candidate, chemicals, entity, therapeutic agents, 1E9M - Small molecules, in vitro, novel active compounds, 1E9M - Targeted hit library, entities collection, 1E9M - In-vitro, vendors, providers, distributors, cro, medicinal chemists, 1E9M - Diverse range, structurally diverse building blocks, hit rich collection, synthesized, 1E9M - Develop new focused arrays in areas of research based on our privileged scaffolds profile, profiling, pre-screened, 1E9M - Methods and principles in medicinal chemistry, computational chemistry, subset of, 1E9M - Broad variety of organic compounds, diversity analysis, synthetic tractability and drug like properties, alkaloids, steroids, 1E9M - Flavonoids, coumarins, terpenoids, sesquiterpene lactones, 1E9M - Glycosides, peptides, purines,pyrimidines, antivirals, antibacterials, tuberculostatics,anti-infectives, 1E9M - Anti-inflammatory, agents, cancerostatics, antidiabetics, cardiovascular, activity, hypo/hypertensives, neurotropic agents, computer-aided, 1E9M - Optimization, prediction,bio-effect, combinatorial chemistry, plant protection, crop, 1E9M - Combinatorial library, potential hits/leads, targeted sub-array,nearest analogs, 1E9M - Structural-topological characteristics, bioeffect, fungistatics, antidiuretics, immunostimulants,parasitocides, antipyretics, psychostimulants, psychomimetics,antirheumatics, tuberculostatics, antiulcer agents, virulicides, 1E9M - 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