• 2D-MH

  • Referenced in 21 articles [sw19727]
  • incorporating the information of the side-chain mass of each of the constituent amino acids...
  • SCWRL4

  • Referenced in 7 articles [sw22393]
  • Improved prediction of protein side-chain conformations with SCWRL4. SCWRL4 is based...
  • BetaSCP

  • Referenced in 3 articles [sw08772]
  • Protein structure optimization by side-chain positioning via beta-complex. A molecular structure determines ... protein structure is the optimization of side-chains called the side-chain positioning problem ... side-chain positioning problem, assuming the rigidity of backbone and a rotamer library, attempts ... moderate-sized proteins because the side-chain positioning problem is NP-hard. On the other...
  • Osprey

  • Referenced in 3 articles [sw21400]
  • flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational...
  • RASP

  • Referenced in 2 articles [sw24067]
  • conformation prediction, we present a RApid Side-chain Predictor, called RASP. To achieve a much...
  • BetaSCPWeb

  • Referenced in 1 article [sw20703]
  • BetaSCPWeb: Side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization. Many applications ... prediction of a protein’s optimal side-chain conformations from just its amino acid sequence ... backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here...
  • GalaxyDock

  • Referenced in 2 articles [sw32096]
  • that allows flexibility of pre-selected side-chains of ligand using Conformational Space Annealing. Binary...
  • SOCKET

  • Referenced in 2 articles [sw35513]
  • recognises the characteristic knobs-into-holes side-chain packing of coiled coils; this proved...
  • BetaSCP2

  • Referenced in 1 article [sw09840]
  • program for the optimal prediction of side-chains in proteins. The side-chain prediction problem...
  • TUNE

  • Referenced in 1 article [sw35757]
  • predict compatibility of amino acid side-chains with structural environments. Log-odds scores of predicted...
  • SPARTA+

  • Referenced in 1 article [sw15078]
  • protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current...
  • SFCHECK

  • Referenced in 1 article [sw16888]
  • considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms...
  • LOOPER

  • Referenced in 1 article [sw17376]
  • only. Construction and optimization of the side-chain conformations is followed by a final ranking...
  • LEDA

  • Referenced in 261 articles [sw00509]
  • In the core computer science areas -- data structures...
  • CPLEX

  • Referenced in 2583 articles [sw04082]
  • IBM® ILOG® CPLEX® offers C, C++, Java, .NET...
  • CHARMM

  • Referenced in 115 articles [sw05953]
  • CHARMM (Chemistry at HARvard Macromolecular Mechanics). CHARMM models...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • RAPTOR: optimal protein threading by linear programming. This...
  • BALL

  • Referenced in 5 articles [sw10727]
  • BALL - Biochemical Algorithms Library: Rapid Software Prototyping can...
  • BULL!

  • Referenced in 2 articles [sw25439]
  • BULL! -- the molecular geometry engine based on Voronoi...
  • GPCR-CA

  • Referenced in 35 articles [sw25949]
  • GPCR-CA: A cellular automaton image approach for...