• HSMUCE

  • Referenced in 13 articles [sw27013]
  • transmembrane protein in the bacterial outer membrane with pronounced heterogeneity for its states...
  • SOSUI

  • Referenced in 8 articles [sw35979]
  • classification and secondary structure prediction system for membrane proteins. The system SOSUI for the discrimination ... membrane proteins and soluble ones together with the prediction of transmembrane helices was developed...
  • OpenCMISS

  • Referenced in 11 articles [sw11475]
  • currents that flow through the cardiac cell membranes. In this paper we discuss the design...
  • Gpos-PLoc

  • Referenced in 11 articles [sw26870]
  • extracell, (4) periplasm and (5) plasma membrane. To eliminate redundancy and homology bias, only those...
  • PDB-REPRDB

  • Referenced in 5 articles [sw26865]
  • residues. The number of entries including membrane protein structures in the PDB has increased rapidly ... with determination of numbers of membrane protein structures because of improved X-ray crystallography ... protein structure studies must address globular and membrane proteins separately, this new elimination factor, which ... excludes membrane protein chains, is introduced in the PDB-REPRDB system. Moreover, the PDB-REPRDB...
  • PRED-TMBB

  • Referenced in 5 articles [sw11338]
  • predicting the topology of beta-barrel outer membrane proteins. In this work we developed ... strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from ... redundant database consisting of 16 outer membrane proteins (OMP’s) with their structures known ... discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets...
  • LMNtal

  • Referenced in 9 articles [sw07312]
  • uses logical variables to represent connectivity and membranes to represent hierarchy. LMNtal is an outcome...
  • SubMito-PSPCP

  • Referenced in 6 articles [sw22432]
  • overall accuracy, with 98.60% for inner membrane, 93.90% for matrix, and 70.70% for outer membrane...
  • Cyto-Sim

  • Referenced in 5 articles [sw35368]
  • formal language model and stochastic simulator of membrane-enclosed biochemical processes. Results: We present Cyto ... stochastic simulator of membrane-enclosed hierarchies of biochemical processes, where the membranes comprise an inner...
  • Apbsmem

  • Referenced in 4 articles [sw22298]
  • graphical interface for electrostatic calculations at the membrane. Electrostatic forces are one of the primary ... these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS ... routines that introduce the influence of the membrane, determine its placement relative to the protein ... membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted...
  • MeCoSim

  • Referenced in 8 articles [sw14527]
  • phenomena by means of P System. MeCoSim (Membrane Computing Simulator) is a software that offers...
  • SGN Sim

  • Referenced in 8 articles [sw29325]
  • reactions within a compartmentalized environment where membrane crossing is controlled by a negative feedback mechanism...
  • cryoSPARC

  • Referenced in 8 articles [sw39533]
  • biologically important targets, with advanced tools for membrane proteins, heterogeneous samples, and flexible molecules. Process...
  • TopologyNet

  • Referenced in 8 articles [sw41013]
  • binding affinities, globular protein mutation impacts, and membrane protein mutation impacts...
  • PSLpred

  • Referenced in 5 articles [sw35525]
  • were attained for cytoplasmic, extracellular, inner-membrane, outer-membrane and periplasmic proteins, respectively. Furthermore, PSLpred...
  • GPCRpred

  • Referenced in 7 articles [sw22471]
  • largest superfamilies of membrane proteins and are important targets for drug design. In this study...
  • BOMP

  • Referenced in 4 articles [sw11337]
  • program to predict integral β-barrel outer membrane proteins encoded within genomes of Gram-negative ... bacterium is an integral β-barrel outer membrane protein. The program, called the β-barrel ... Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral...
  • MPRAP

  • Referenced in 3 articles [sw35228]
  • MPRAP is a novel Membrane Protein Residue Accessibility Predictor, based on sequence derived information ... contrast to previous membrane predictors, MPRAP, performs well both within and outside the membrane regions ... outperforms earlier methods in the membrane regions: MPRAP: An accessibility predictor for a-helical transmem ... that performs well inside and outside the membrane...
  • pLinguaCore

  • Referenced in 6 articles [sw06894]
  • formats. This library reports the rules and membrane structure read from a file where...
  • pSLIP

  • Referenced in 6 articles [sw35549]
  • chloroplast, cytoplasmic, extracellular, mitochondrial, nuclear and plasma membrane. The algorithm was applied to the dataset...