• Osprey

  • Referenced in 3 articles [sw21400]
  • protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that...
  • Frustratometer

  • Referenced in 3 articles [sw27727]
  • energy is distributed in protein structures and how mutations or conformational changes shift the energy ... allows to calculate frustration on much larger protein structures and multimers. Additionally the effect...
  • GANM

  • Referenced in 1 article [sw08551]
  • achieve protein-ligand docking simulations that take into account global and local conformational adjustments ... account for the global conformational changes of the protein. This software is implemented in distinct...
  • CAVER

  • Referenced in 1 article [sw20702]
  • conformations needed to properly describe conformational space of protein structure. In this paper, we describe...
  • FATCAT

  • Referenced in 3 articles [sw32830]
  • server returns a list of protein structures that are similar to the query, ordered ... report the conformational changes of the query structure as compared to other proteins...
  • PreSSAPro

  • Referenced in 2 articles [sw00730]
  • perspective of identifying proteins able to fold in different conformations. The service is available...
  • 3DIGARS

  • Referenced in 1 article [sw36904]
  • Energy Function and Effective Conformational Search Strategy based ab initio Protein Structure Prediction. To solve ... protein structure prediction (PSP) problems computationally, a plethora of template-based methods exist. However, there ... distribution have been utilized to guide the conformation search. Crucial features, such as sequence-specific ... hydrophobic-hydrophilic properties and torsion angles of protein residues are mined to formulate an optimized...
  • TMBpro

  • Referenced in 5 articles [sw11341]
  • modeling methods, however, fail on most TMB proteins since very few non-homologous TMB structures ... have been determined. Yet, because TMB structures conform to specific construction rules that restrict...
  • TRAJELIX

  • Referenced in 1 article [sw10942]
  • Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. We have ... geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially...
  • ConsDock

  • Referenced in 1 article [sw09660]
  • accuracy for both the protein-bound orientation and the conformation of the ligand ... applied to a test set of 100 protein-ligand complexes from the Protein Data Bank...
  • NSOL

  • Referenced in 2 articles [sw21620]
  • simulation of proteins and nucleic acids, such as MD and/or MC, conformational energy + solvation energy...
  • CHARMM36m

  • Referenced in 1 article [sw35721]
  • disordered proteins. The all-atom additive CHARMM36 protein force field is widely used in molecular ... generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins...
  • BetaSCPWeb

  • Referenced in 1 article [sw20703]
  • prediction of a protein’s optimal side-chain conformations from just its amino acid sequence...
  • DISCO

  • Referenced in 7 articles [sw13152]
  • DISCO -- a MATLAB software for distributed conformation of anchor-free graph realization problems ... applied to the problem of determining protein moleculer structure. Tests are performed on molecules taken ... from the Protein Data Bank database. For each molecule, given 20–30% of the inter ... able to reliably and efficiently reconstruct the conformation of large molecules. In particular, given...
  • SODOCK

  • Referenced in 4 articles [sw32098]
  • optimization for highly flexible protein-ligand docking. Protein-ligand docking can be formulated ... aims to identify the translation, orientation, and conformation of a docked ligand with the lowest ... particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. To improve efficiency...
  • UniCon3D

  • Referenced in 0 articles [sw34253]
  • UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling ... residue representation and performs experimentally motivated conditional conformational sampling via stepwise synthesis and assembly ... knowledge-based energy function for de novo protein structure prediction. The proposed method, UniCon3D ... conformations with higher accuracy than traditional random sampling in a small benchmark of 6 proteins...
  • SPARTA+

  • Referenced in 1 article [sw15078]
  • chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields ... shifts for a set of eleven validation proteins. These results represent a modest but consistent...
  • AGGRESCAN

  • Referenced in 3 articles [sw22400]
  • CONCLUSION: By identifying aggregation-prone segments in proteins, AGGRESCAN http://bioinf.uab.es/aggrescan/ shall facilitate ... therapeutic targets for anti-depositional strategies in conformational diseases and (ii) the anticipation of aggregation...
  • GalaxyDock

  • Referenced in 2 articles [sw32096]
  • GalaxyDock is a protein-ligand docking program that allows flexibility of pre-selected side-chains ... ligand using Conformational Space Annealing. Binary executible files (can be run linux and MACOSX system...
  • ProDy

  • Referenced in 4 articles [sw24072]
  • given family or subfamily of proteins, their mutants and sequence homologues, in the presence/absence ... visualization of the principal changes in conformations that are accessible in different functional states. ProDy...