• PDB2PQR

  • Referenced in 33 articles [sw13087]
  • manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific substitution tables have been...
  • SCWRL4

  • Referenced in 7 articles [sw22393]
  • rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft...
  • LIGPLOT

  • Referenced in 5 articles [sw16869]
  • intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. The program...
  • PROMOTIF

  • Referenced in 5 articles [sw26864]
  • loops; disulphide bridges; and main-chain hydrogen bonding patterns. PROMOTIF creates postscript files showing...
  • STRIDE

  • Referenced in 4 articles [sw33184]
  • algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle...
  • NuSol

  • Referenced in 2 articles [sw16826]
  • Schrödinger equation. The classification of short hydrogen bonds depends on several factors including the shape ... spacing between the nuclear eigenstates of the hydrogen. par Here, we describe the NuSol program ... oscillators and applied them to study hydrogen bonding in the malonaldehyde derivate 4-cyano...
  • PConPy

  • Referenced in 2 articles [sw23591]
  • protein contact maps, distance maps and hydrogen bond plots. These maps can be generated ... annotated with secondary structure and hydrogen bond assignments. PConPy offers a more flexible choice...
  • MetaPSICOV

  • Referenced in 1 article [sw17012]
  • prediction of contacts and long range hydrogen bonding in proteins. Motivation: Recent developments of statistical ... predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor ... PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision ... hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. Availability and implementation: MetaPSICOV...
  • DecoyFinder

  • Referenced in 1 article [sw16043]
  • have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value...
  • Mdtraj

  • Referenced in 2 articles [sw22742]
  • tons of analysis functions like bonds/angles/dihedrals, hydrogen bonding identification, secondary structure assignment, NMR observables...
  • PAComplex

  • Referenced in 2 articles [sw21769]
  • displays detailed interacting models (e.g. hydrogen bonds and steric interactions in two interfaces) of hitTCR...
  • DL_ANALYSER

  • Referenced in 1 article [sw37768]
  • identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through ... head-to-tail” conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen...
  • LUDI

  • Referenced in 1 article [sw24443]
  • enzyme) in such a way that hydrogen bonds can be formed with the enzyme ... positions in space suitable to form hydrogen bonds or to fill a hydrophobic pocket...
  • COILCHECK

  • Referenced in 1 article [sw30036]
  • interactions and for the presence of hydrogen bonds and salt bridges. The sum of these...
  • MANIP

  • Referenced in 1 article [sw25064]
  • displays the allowed and nonallowed hydrogen bonds between the residues. The program is interfaced with...
  • WIWS

  • Referenced in 1 article [sw20958]
  • optimization, adding hydrogens and optimizing hydrogen bonds and a series of geometric calculations. The freely...
  • STING contacts

  • Referenced in 1 article [sw35653]
  • types by GC and IFRgc include hydrogen bonds (in nine different flavors), hydrophobic interactions, charge...
  • MINT

  • Referenced in 1 article [sw16407]
  • conformation MINT determines the hydrogen bonding network resolving the base pairing patterns, identifies secondary structure...
  • CONFOLD

  • Referenced in 1 article [sw17008]
  • structures into distance, dihedral angle, and hydrogen bond restraints according...