J Chem Inf Model - Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem.

Tópicos

{ model(3480) simul(1196) paramet(876) }
{ method(984) reconstruct(947) comput(926) }
{ bind(1733) structur(1185) ligand(1036) }
{ activ(1138) subject(705) human(624) }
{ drug(1928) target(777) effect(648) }
{ problem(2511) optim(1539) algorithm(950) }
{ algorithm(1844) comput(1787) effici(935) }
{ compound(1573) activ(1297) structur(1058) }
{ research(1218) medic(880) student(794) }
{ first(2504) two(1366) second(1323) }
{ structur(1116) can(940) graph(676) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ studi(2440) review(1878) systemat(933) }
{ data(1714) softwar(1251) tool(1186) }
{ case(1353) use(1143) diagnosi(1136) }
{ research(1085) discuss(1038) issu(1018) }
{ visual(1396) interact(850) tool(830) }
{ state(1844) use(1261) util(961) }
{ cost(1906) reduc(1198) effect(832) }
{ data(3008) multipl(1320) sourc(1022) }
{ analysi(2126) use(1163) compon(1037) }
{ use(976) code(926) identifi(902) }
{ process(1125) use(805) approach(778) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ network(2748) neural(1063) input(814) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ assess(1506) score(1403) qualiti(1306) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ studi(1119) effect(1106) posit(819) }
{ health(3367) inform(1360) care(1135) }
{ gene(2352) biolog(1181) express(1162) }
{ can(981) present(881) function(850) }
{ survey(1388) particip(1329) question(1065) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ design(1359) user(1324) use(1319) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ activ(1452) weight(1219) physic(1104) }

Resumo

The derivation and optimization of most energy terms in modern force fields are aided by automated computational tools. It is therefore important to have algorithms to rapidly and precisely train large numbers of interconnected parameters to allow investigators to make better decisions about the content of molecular models. In particular, the traditional approach to deriving dihedral parameters has been a least-squares fit to target conformational energies through variational optimization strategies. We present a computational approach for simultaneously fitting force field dihedral amplitudes and phase constants which is analytic within the scope of the data set. This approach completes the optimal molecular mechanics representation of a quantum mechanical potential energy surface in a single linear least-squares fit by recasting the dihedral potential into a linear function in the parameters. We compare the resulting method to a genetic algorithm in terms of computational time and quality of fit for two simple molecules. As suggested in previous studies, arbitrary dihedral phases are only necessary when modeling chiral molecules, which include more than half of drugs currently in use, so we also examined a dihedral parametrization case for the drug amoxicillin and one of its stereoisomers where the target dihedral includes a chiral center. Asymmetric dihedral phases are needed in these types of cases to properly represent the quantum mechanical energy surface and to differentiate between stereoisomers about the chiral center.

Resumo Limpo

deriv optim energi term modern forc field aid autom comput tool therefor import algorithm rapid precis train larg number interconnect paramet allow investig make better decis content molecular model particular tradit approach deriv dihedr paramet leastsquar fit target conform energi variat optim strategi present comput approach simultan fit forc field dihedr amplitud phase constant analyt within scope data set approach complet optim molecular mechan represent quantum mechan potenti energi surfac singl linear leastsquar fit recast dihedr potenti linear function paramet compar result method genet algorithm term comput time qualiti fit two simpl molecul suggest previous studi arbitrari dihedr phase necessari model chiral molecul includ half drug current use also examin dihedr parametr case drug amoxicillin one stereoisom target dihedr includ chiral center asymmetr dihedr phase need type case proper repres quantum mechan energi surfac differenti stereoisom chiral center

Resumos Similares

Comput Math Methods Med - A meshfree method for simulating myocardial electrical activity. ( 0,739179100650247 )
Comput Math Methods Med - Complexity analysis and parameter estimation of dynamic metabolic systems. ( 0,716782088386361 )
Comput Math Methods Med - Modeling schistosomiasis and HIV/AIDS codynamics. ( 0,70712076654629 )
Neural Comput - Computing confidence intervals for point process models. ( 0,702275851817742 )
Comput Biol Chem - An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology. ( 0,69348587373251 )
Comput Math Methods Med - Numerical solutions for a model of tissue invasion and migration of tumour cells. ( 0,692817407503628 )
Comput Methods Programs Biomed - Reprint of Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin. ( 0,687619428023219 )
Brief. Bioinformatics - Choosing appropriate models for protein-protein interaction networks: a comparison study. ( 0,684349824836975 )
Neural Comput - Effect of phase response curve skewness on synchronization of electrically coupled neuronal oscillators. ( 0,683348456271836 )
Comput Math Methods Med - Analytical solutions for the mathematical model describing the formation of liver zones via Adomian's method. ( 0,68299219518854 )
Comput. Biol. Med. - Numerical investigation into blood clotting at the bone-dental implant interface in the presence of an electrical stimulus. ( 0,681840198763484 )
Comput. Biol. Med. - Phase lagging model of brain response to external stimuli-modeling of single action potential. ( 0,67826576556613 )
Comput. Biol. Med. - Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of A? peptide. ( 0,671401788880201 )
J Chem Inf Model - Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations. ( 0,668411563317504 )
Comput Math Methods Med - Dynamics analysis and simulation of a modified HIV infection model with a saturated infection rate. ( 0,668027938557177 )
Neural Comput - Cross-talk induces bifurcations in nonlinear models of synaptic plasticity. ( 0,665388273699876 )
Comput Methods Programs Biomed - Development of a computer algorithm for feedback controlled electrical nerve fiber stimulation. ( 0,660989141794039 )
Comput. Biol. Med. - Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics. ( 0,658670690527488 )
J Integr Bioinform - An advanced environment for hybrid modeling of biological systems based on modelica. ( 0,658539072092534 )
Comput. Biol. Med. - Modelling and simulating reaction-diffusion systems using coloured Petri nets. ( 0,654737089104566 )
Comput. Biol. Med. - ODE/PDE analysis of corneal curvature. ( 0,650286954616289 )
J. Comput. Biol. - Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible? ( 0,648378892583904 )
Comput Math Methods Med - Modeling innate immune response to early Mycobacterium infection. ( 0,646723455874155 )
Med Biol Eng Comput - CSF dynamic analysis of a predictive pulsatility-based infusion test for normal pressure hydrocephalus. ( 0,643599097775718 )
J Chem Inf Model - Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. ( 0,643394319350984 )
J. Comput. Biol. - Exploring the landscape of protein-ligand interaction energy using probabilistic approach. ( 0,636810474280517 )
IEEE Trans Image Process - Geometrically induced force interaction for three-dimensional deformable models. ( 0,636521159746286 )
Comput Math Methods Med - Global hopf bifurcation on two-delays leslie-gower predator-prey system with a prey refuge. ( 0,631711912529651 )
Comput Math Methods Med - Solid dynamic models for analysis of stress and strain in human hearts. ( 0,629519411972024 )
Comput Math Methods Med - Solutions of a linearized mathematical model for capillary formation in tumor angiogenesis: an initial data perturbation approximation. ( 0,629426204244916 )
Comput Math Methods Med - ModeLang: a new approach for experts-friendly viral infections modeling. ( 0,629304182988073 )
Comput Math Methods Med - Computational modeling of microabscess formation. ( 0,629115365073544 )
Comput. Biol. Med. - Network and Nakamura tridiagonal computational simulation of electrically-conducting biopolymer micro-morphic transport phenomena. ( 0,628551792485591 )
Comput Math Methods Med - Numerical stability of partitioned approach in fluid-structure interaction for a deformable thin-walled vessel. ( 0,625629253920881 )
Lifetime Data Anal - An extended cure model and model selection. ( 0,625058052125926 )
Neural Comput - Neural dynamics, bifurcations, and firing rates in a quadratic integrate-and-fire model with a recovery variable. I: Deterministic behavior. ( 0,622818352378733 )
Comput Biol Chem - A stochastic evolution model for residue Insertion-Deletion Independent from Substitution. ( 0,621528855811105 )
Comput Methods Programs Biomed - An efficient passive planar micromixer with ellipse-like micropillars for continuous mixing of human blood. ( 0,621486119083404 )
Neural Comput - Analytical integrate-and-fire neuron models with conductance-based dynamics and realistic postsynaptic potential time course for event-driven simulation strategies. ( 0,621225869338033 )
Comput Math Methods Med - Hybrid mesh for nasal airflow studies. ( 0,621042450683114 )
Comput Methods Programs Biomed - Parametric-based brain Magnetic Resonance Elastography using a Rayleigh damping material model. ( 0,620929163129896 )
J Chem Inf Model - Molecular dynamic simulations of ocular tablet dissolution. ( 0,620413984856682 )
Comput Methods Programs Biomed - Functionality of the baroreceptor nerves in heart rate regulation. ( 0,618562130020105 )
Neural Comput - Active data collection for efficient estimation and comparison of nonlinear neural models. ( 0,617310134087234 )
Comput. Biol. Med. - Computing the stability of steady-state solutions of mathematical models of the electrical activity in the heart. ( 0,614956285635439 )
IEEE Trans Image Process - Geometric flow approach for region-based image segmentation. ( 0,614543092317464 )
Comput Math Methods Med - The stochastic evolution of a protocell: the Gillespie algorithm in a dynamically varying volume. ( 0,613902188600278 )
Comput Methods Programs Biomed - Solving delay differential equations in S-ADAPT by method of steps. ( 0,613746529053083 )
Comput. Biol. Med. - Semi-computational simulation of magneto-hemodynamic flow in a semi-porous channel using optimal homotopy and differential transform methods. ( 0,610563543361447 )
J Chem Inf Model - Conformational analysis of aliskiren, a potent renin inhibitor, using high-resolution nuclear magnetic resonance and molecular dynamics simulations. ( 0,609847747735295 )
Neural Comput - Toward unified hybrid simulation techniques for spiking neural networks. ( 0,608301561960805 )
J Chem Inf Model - Theoretical prediction of hydrogen-bond basicity pKBHX using quantum chemical topology descriptors. ( 0,607468638856284 )
Comput Math Methods Med - A theoretical model for the transmission dynamics of the Buruli ulcer with saturated treatment. ( 0,605870073044244 )
IEEE Trans Image Process - Reinitialization-free level set evolution via reaction diffusion. ( 0,605650061501524 )
Med Biol Eng Comput - A fluid-structure interaction model of the aortic valve with coaptation and compliant aortic root. ( 0,605101561509964 )
Comput Math Methods Med - Theoretical Hill-type muscle and stability: numerical model and application. ( 0,604575498988628 )
J Chem Inf Model - New model of cystic fibrosis transmembrane conductance regulator proposes active channel-like conformation. ( 0,602281699702336 )
IEEE Trans Vis Comput Graph - Paraglide: Interactive Parameter Space Partitioning for Computer Simulations. ( 0,600962141576043 )
Int J Neural Syst - A generalized Leaky Integrate-and-Fire neuron model with fast implementation method. ( 0,60076029057829 )
Comput Math Methods Med - Uncertainty quantification in simulations of epidemics using polynomial chaos. ( 0,599392488548473 )
Comput Methods Programs Biomed - Kinetic modelling of the role of the aldehyde dehydrogenase enzyme and the breast cancer resistance protein in drug resistance and transport. ( 0,597998328134853 )
Comput. Biol. Med. - An implicit evolution scheme for active contours and surfaces based on IIR filtering. ( 0,597017654730048 )
Comput Math Methods Med - Noninvasive monitoring of hepatic damage from hepatitis C virus infection. ( 0,595732358131272 )
Comput Methods Programs Biomed - Innovative model to simulate exhalation phase in human respiratory system. ( 0,595115036360841 )
IEEE Trans Image Process - Fast cartoon + texture image filters. ( 0,595011564116568 )
Comput. Biol. Med. - Volume conductor models in surface electromyography: computational techniques. ( 0,594166487360707 )
Neural Comput - Theoretical and evolutionary parameter tuning of neural oscillators with a double-chain structure for generating rhythmic signals. ( 0,593910572791426 )
Comput Methods Programs Biomed - Modelling the Double Peak Phenomenon in pharmacokinetics. ( 0,592516623705267 )
Comput Math Methods Med - Simulations of complex and microscopic models of cardiac electrophysiology powered by multi-GPU platforms. ( 0,591534071964135 )
Comput. Biol. Med. - Examples of testing global identifiability of biological and biomedical models with the DAISY software. ( 0,591265892744704 )
J Chem Inf Model - Free energy predictions of ligand binding to an a-helix using steered molecular dynamics and umbrella sampling simulations. ( 0,589406013503929 )
Comput Math Methods Med - Towards patient-specific modeling of coronary hemodynamics in healthy and diseased state. ( 0,588761567309142 )
IEEE Trans Image Process - Efficiency of semi-implicit schemes for anisotropic diffusion in the hypercube. ( 0,588062174113051 )
Comput. Biol. Med. - epiModel: a system to build automatically systems of differential equations of compartmental type-epidemiological models. ( 0,587557993611956 )
J Clin Monit Comput - The standard strong ion difference, standard total titratable base, and their relationship to the Boston compensation rules and the Van Slyke equation for extracellular fluid. ( 0,58597069499732 )
Wiley Interdiscip Rev Syst Biol Med - A conceptual framework for computational models of Achilles tendon homeostasis. ( 0,58573113703416 )
IEEE Trans Image Process - Box relaxation schemes in staggered discretizations for the dual formulation of total variation minimization. ( 0,58563037728316 )
J Chem Inf Model - Multiscale macromolecular simulation: role of evolving ensembles. ( 0,58511258535809 )
J Chem Inf Model - Electronic structure investigation and parametrization of biologically relevant iron-sulfur clusters. ( 0,584149487233058 )
IEEE Trans Neural Netw Learn Syst - Discrete-Time Zhang Neural Network for Online Time-Varying Nonlinear Optimization With Application to Manipulator Motion Generation. ( 0,583829987908728 )
Comput. Biol. Med. - Density-based Monte Carlo filter and its applications in nonlinear stochastic differential equation models. ( 0,583278226504687 )
IEEE Trans Vis Comput Graph - Anisotropic Elliptic PDEs for Feature Classification. ( 0,583270688187375 )
Comput Math Methods Med - Optimisation of a generic ionic model of cardiac myocyte electrical activity. ( 0,582820751285844 )
Comput Methods Programs Biomed - Numerical framework to model temporally resolved multi-stage dynamic systems. ( 0,582554106763673 )
J Chem Inf Model - Practical considerations for building GROMOS-compatible small-molecule topologies. ( 0,580583926172221 )
Comput Methods Programs Biomed - Feedback controlled electrical nerve stimulation: a computer simulation. ( 0,580278592668488 )
Brief. Bioinformatics - LC-MS alignment in theory and practice: a comprehensive algorithmic review. ( 0,579634381303715 )
Wiley Interdiscip Rev Syst Biol Med - Influenza A virus infection kinetics: quantitative data and models. ( 0,579199740528288 )
Neural Comput - Functional identification of spike-processing neural circuits. ( 0,579025950353928 )
Comput Methods Programs Biomed - System approach to modeling of liver glucose metabolism with physiologically interpreted model parameters outgoing from [18F]FDG concentrations measured by PET. ( 0,578970483742525 )
J Chem Inf Model - Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects. ( 0,577395943828295 )
Med Biol Eng Comput - Computational modeling of the human atrial anatomy and electrophysiology. ( 0,576462665631226 )
IEEE Trans Image Process - Additive log-logistic model for networked video quality assessment. ( 0,574377886879296 )
Comput. Biol. Med. - Simulated temperature distribution of the proximal forearm. ( 0,574061969506194 )
Comput Math Methods Med - Spongiosa primary development: a biochemical hypothesis by Turing patterns formations. ( 0,57357282168813 )
J Chem Inf Model - Comparison of resonance assisted and charge assisted effects in strengthening of hydrogen bonds in dipyrrins. ( 0,573428882470235 )
Comput Methods Programs Biomed - Numerical and experimental analysis of factors leading to suture dehiscence after Billroth II gastric resection. ( 0,571266502914695 )
Med Biol Eng Comput - Experimental parameter identification of a multi-scale musculoskeletal model controlled by electrical stimulation: application to patients with spinal cord injury. ( 0,571145669590955 )
Neural Comput - Dynamical movement primitives: learning attractor models for motor behaviors. ( 0,569796391882818 )
Comput Math Methods Med - Global stability of HIV infection of CD4+ T cells and macrophages with CTL immune response and distributed delays. ( 0,569205400350816 )