• CHARMM

  • Referenced in 112 articles [sw05953]
  • classical mechanical methods to investigate potential energy surfaces derived from experimental and ”ab initio” quantum...
  • ABS

  • Referenced in 26 articles [sw21211]
  • functional language for modeling data. ABS uses asynchronous method calls, interfaces for encapsulation, and cooperative ... scheduling of method activations inside concurrent objects. This feature combination results in a concurrent object ... compositional. We discuss central design issues for ABS and formalize the type system and semantics ... particular, “method not understood” errors do not occur at runtime for well-typed ABS models...
  • transiesta

  • Referenced in 5 articles [sw33754]
  • nonequilibrium electron transport. We describe an ab initio method for calculating the electronic structure, electronic ... scattering states. As an illustration, the method is applied to three systems where ... ab initio DFT calculations or experiments, and we point out differences between this method...
  • SIESTA

  • Referenced in 22 articles [sw05949]
  • method and its computer program implementation, to perform efficient electronic structure calculations and ab initio ... systems with some first-principles electronic-structure methods has opened up new opportunities in many...
  • SHRiMP

  • Referenced in 15 articles [sw17146]
  • separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space...
  • MOLPRO

  • Referenced in 19 articles [sw06125]
  • MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations, designed ... multiconfiguration-reference CI, coupled cluster and associated methods. The recently developed explicitly correlated coupled-cluster ... methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab...
  • SMEAGOL

  • Referenced in 5 articles [sw33755]
  • atomically generated orbital landscapes. Ab initio computational methods for electronic transport in nanoscaled systems...
  • PreDisorder

  • Referenced in 2 articles [sw16902]
  • based on our ab initio prediction method (MULTICOM-CMFR) which, along with our meta ... consensus) prediction method (MULTICOM), was recently ranked among the top disorder predictors in the eighth ... that it compared favourably with other ab initio methods and its performance is comparable...
  • PRED-CLASS

  • Referenced in 5 articles [sw26873]
  • several organisms demonstrates that such a method could serve as a valuable tool ... step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various...
  • JiABS

  • Referenced in 1 article [sw07297]
  • Numerical analysis of integer ABS methods The authors provide the first detailed numerical analysis ... implementation) of the scaled non-symmetric integer ABS algorithm (snsiABS) algorithm to be the fastest...
  • RVMAB

  • Referenced in 1 article [sw24037]
  • propose a novel computational method called RVM-AB that combines the Relevance Vector Machine ... protein sequences. Firstly, Average Blocks (AB) feature extraction method is employed to represent protein sequences ... Component Analysis (PCA) method is used to reduce the dimension of AB vector for reducing ... other previous methods. The experimental results proved that our RVM-AB prediction model is efficiency...
  • DeepQA

  • Referenced in 1 article [sw15927]
  • introduce a novel single-model quality assessment method DeepQA based on deep belief network that ... models generated by our in-house ab initio method. Our experiment demonstrate that deep belief ... dataset. It also outperformed two well-established methods in selecting good outlier models from ... mostly low quality generated by ab initio modeling methods. DeepQA is a useful tool...
  • LiPsMin

  • Referenced in 2 articles [sw26236]
  • robust optimization. This paper presents a minimization method for Lipschitz continuous, piecewise smooth objective functions ... nondifferentiabilities are caused by abs(), min(), and max(). The optimization method generates successively piecewise linearizations ... kink structure. Both the generation of the abs-normal form and the exploitation ... comparison of LiPsMin with other nonsmooth optimization methods are discussed...
  • ALTDSE

  • Referenced in 4 articles [sw00037]
  • describe a general ab initio and non-perturbative method to solve the time-dependent Schrödinger...
  • LOOPER

  • Referenced in 1 article [sw17376]
  • loop prediction. We describe a new ab initio method and corresponding program, LOOPER ... prediction of protein loop conformations. The method is based on a multi-step algorithm (developed ... scoring. One of the main obstacles to ab initio computational loop modeling is the exponential ... loop fragment. In contrast to many ab initio algorithms that use Monte-Carlo schemes...
  • DNADU

  • Referenced in 1 article [sw23315]
  • genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements ... clearly understood. We present an {it ab initio} method to quantitatively detect repetitive elements...
  • CFOUR

  • Referenced in 1 article [sw27006]
  • rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic...
  • TSIG_COMP

  • Referenced in 1 article [sw12501]
  • modify the spectral patterns. To date, ab initio methods are incapable of taking these effects...
  • GAMESS

  • Referenced in 34 articles [sw03002]
  • GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute ... orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated...
  • REL4D

  • Referenced in 1 article [sw24378]
  • approach for the relativistic ab initio molecular orbital (MO) methods is reviewed. Emphasis is placed ... integral evaluation methods. Illustrative calculations, performed with a new four-component relativistic ab initio ... Fock (DHF) and Dirac-Hartree-Fock (DKS) methods. Next, in the two-component quasirelativistic framework...