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Text of the page (random words):
erage number of decoys per set reference 4state_reduced 7 665 park levitt 1996 fisa 6 1432 simons et al 1997 fisa_casp3 6 1432 simons et al 1997 hg_structal 29 29 samudrala et al 1998c ig_structal 61 60 samudrala et al 1998c ig_structal_hires 20 19 samudrala et al 1998c lattice_ssfit 8 2000 samudrala et al 1999 xia et al 2000 lmds 11 439 keasar levitt 1999 semfold 6 12900 samudrala levitt 2002 vhp_mcmd 1 6255 fogolari et al 2005 a directory name with the suffix of _u for unrefined indicates that the decoy conformations for a given protein have not been energy minimised in cases where both minimised and unminimised versions of a decoy are provided the bin directory if it exists contains shell scripts or programs that will help manipulation of these decoys the doc directory contains any pertinent documentation the file notes see example in figure 2 contains details about the decoy sets including the primary source the number of decoys and the range of rmsds for each protein a short description any relevant comments and references for particular decoy sets the doc directory contains the original pdb files as available in the protein data bank under the pdb_orig subdirectory figure 2 example of a notes file for the multiple decoy sets this particular file is for the fisa decoy set description the fisa set contains decoys for four small alpha helical proteins the main chains for these decoys were generated using a fragment insertion simulated annealing procedure to assemble native like structures from fragments of unrelated protein structures with similar local sequences using bayesian scoring functions simons et al 1997 primary source side chains for these proteins were modelled with the software package scwrl bower et al 1997 primary source simons kt kooperberg c huang es baker d assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions j mol biol 268 209 225 1997 summary protein crmsd range resolution r reference 1fc2 500 3 111 10 580 2 8 0 22 deisenhofer 1981 1hdd c 500 2 769 12 915 2 8 0 24 kissinger et al 1990 2cro 500 4 288 12 599 2 4 0 20 mondragon et al 1989 4icb 500 4 754 14 130 1 6 0 19 svensson et al 1992 average 500 3 731 12 556 2 4 0 21 comments all conformations were subjected to 500 steps of steepest descent minimusation using the charmm22b force field brooks et al 1983 ignoring electrostatic terms and using a cut off of 12 a for non bonded interactions resolution r factor and reference listed above are details about the experimental structure references bower mj cohen fe dunbrack rl prediction of protein side chain rotamer from a backbone dependent rotamer library a new homology modelling tool j mol biol 267 1268 1282 1997 brooks br bruccoleri re olafson bd states dj swaminathan s karplus m charmm a program for macromolecular energy minimisation and dynamics calculations j comput chem 4 187 217 1994 deisenhofer j crystallographic refinement and atomic models of a human fc fragment and its complex with fragment b of protein a from staphylococcus aureus at 2 9 and 2 8 angstroms resolution biochemistry 20 2361 2370 1981 kissinger cr liu bs martin blanco e kornberg tb pabo co crystal structure of an engrailed homeodomain dna complex at 2 8 a resolution a framework for understanding homeodomain dna interactions cell 63 579 590 1990 mondragon a wolberger c harrison sc structure of phage 434 cro protein at 2 35 angstroms resolution j mol biol 205 179 188 1989 svensson la thulin e forsen s proline cis trans isomers in calbindin observed by x ray crystallography j mol biol 223 601 606 1992 the single decoy sets the single decoy sets are listed in table 2 there is a directory for each single decoy set under dd single within that directory are two directories correct and incorrect which respectively contain the correct and the corresponding incorrect conformations for a given protein also included in both directories is a file called list which lists the conformation pdb files in those directories the mapping of the list files in the correct and incorrect directories is 1 1 even if there are fewer correct conformations than incorrect conformations table 2 single decoy sets to download a particular set click on the name of the set click here to download all the single decoy sets name of set number of proteins decoys reference misfold 26 holm sander 1992 pdb_error 3 branden jones 1990 as with the multiple decoy sets doc and bin serve to provide additional documentation and executables to make processing of a given set easier also the doc pdb_orig directory contains the original experimental structures the format of the notes file is slightly different than that used for the multiple decoy sets see example in figure 3 here the rmsd ranges are omitted but a summary line is provided for each correct and incorrect decoy conformation figure 3 example of a notes file for single decoy sets this particular file is for the pdb_error decoy set description the pdb_error set contains coordinates for pairs of experimental structures in cases where one of the pair has been substantially refined or found to contain errors this structure is designated as incorrect primary source there is no primary source as both the correct and incorrect structures are directly obtained from the pdb and are produced by different sources however a general source to cite would be branden jones 1990 summary correct incorrect resolution r reference 2f19 1f19 2 8 0 18 lascombe et al 1992 3hfl 2hfl 2 6 0 29 cohen et al 1995 5fd1 2fd1 1 9 0 21 stout 1993 5rxn 5rxnon1fdx 1 2 0 14 watenpaugh 1984 comments resolution r factor and reference listed above are details about the experimental correct structure the incorrect structures are no longer present in the pdb references branden ci jones ta between objectivity and subjectivity nature 343 687 689 1990 cohen gh sheriff s davies dr the refined structure of the monoclonal antibody hy slash hel 5 with its antigen hen egg white lysozyme to be published 1995 lascombe mb alzari pm poljak rj nisonoff a three dimensional structure of two crystal forms of fab r19 9 from a monoclonal anti arsonate antibody proc natl acad sci usa 89 9429 9433 1992 stout cd crystal structures of oxidized and reduced azotobacter vinelandii ferredoxin at ph 8 and ph 6 j biol chem 268 25920 25927 1993 the loop decoy sets table 3 lists the loop decoy sets the directory name for each loop decoy set under dd loop method loop set takes on the form protein _ start stop start and stop signify the residue ranges for a given loop that varies in conformation for example 3dfr_20 40 all the loop conformations are stored in a single file with the name protein _ start stop loops pdb within the directory for each loop set the file loop_data contains information about the loop containing the range of residues the name of the experimental structure with the right orientation so the loops can just be inserted into the structure the name of the file containing all the loops and the number of lines per loop in that file see example in figure 4 table 2 loop decoy sets to download a particular set click on the name of the set click here to download all the single decoy sets name of set number of sets average number of loops per set reference abm_database 4 200 samudrala moult 1998b figure 4 example of a loop_data file for loop decoy sets this particular file is for the 1vfa_205 212 decoy set 205 212 1vfa pdb 1vfa_205 212 loops pdb 78 in all the loop sets there is only one stretch of sequence that varies the rest of the protein is held constant if more than one stretch varies then the set is considered to belong in the multiple decoy set the bin doc and doc pdb_orig directories serve the the same purpose as in the multiple and single decoy set the format of the notes file is similar to the format used for multiple decoy sets but the summary line information contains details about size and range of the loop residues the sequence the number of loop conformations and the ca rmsd ranges see example in figure 5 figure 5 example of a notes file for loop decoy sets this particular file is for the abm_database set description the abm_database set contains loop conformations for the d1 3 antibody 1vfa the main chains for these loops were generated using a database procedure pedersen et al 1992 side chains were constructed using the program scgen samudrala moult 1998a these loops were generated to test the ability of a graph theoretical clique finding method to select the best set of loop conformations taking the environment context into account samudrala moult 1998 primary source primary source samudrala r moult j a graph theoretic algorithm for comparative modelling of protein structure j mol biol 279 287 302 1998 summary loop size sequence crmsd range resolution r reference 1vfa_47 55 9 lvyytttla 176 0 663 5 287 1 8 0 15 bhat et al 1994 1vfa_90 97 8 hfwstprt 166 0 646 5 247 1 8 0 15 bhat et al 1994 1vfa_158 166 9 miwgdgntd 168 0 402 6 239 1 8 0 15 bhat et al 1994 1vfa_205 212 8 rerdyrld 216 0 458 5 435 1 8 0 15 bhat et al 1994 average 9 182 0 542 5 552 1 8 0 15 comments resolution r factor and reference listed above are details about the experimental structure references bhat tn bentley ga boulot g green mi tello d dall acqua w souchon h schwarz fp mariuzza ra poljak rj bound water molecules and conformational stabilization help mediate an antigen antibody association proc nat acad sci usa 91 1089 1093 1994 pedersen j searle s henry a rees ar antibody modelling beyond homology immunomethods 1 126 136 1992 samudrala r moult j determinants of side chain conformational preferences in protein structures protein eng 1998 in press examples of decoys as mentioned above the goal of this endeavour is to collect decoys which scoring functions cannot distinguish from the native conformation figure 6 illustrates this for two proteins in the lattice_ssfit decoy set figure 6 example of decoys in the lattice_ssfit decoy set shown are decoys for two proteins calbindin pdb code 4icb which is an alpha helical protein and ferrodoxin pdb code 1fca the structures on the far left represent grossly incorrect structures with a good score by different scoring functions structures in the middle are the experimental conformations structures on the far right are selections by an all atom scoring function samudrala moult 1998a all structures depicted above are compact and have the native secondary structure usage guidelines the maintainer has taken great pains to ensure that the people who have submitted decoys have given their permission and have been properly attributed in any effort of this size there are bound to be mistakes if you spot a mistake please let me know so i can fix it as soon as possible if you find any of the decoys useful and use it in a published work please give credit where due also please realise that all the contributors for this database have readily and openly published their work people who use these database and publish their results equally openly would be making the best use of this effort if you wish to contribute decoy sets please contact dd compbio org acknowledgements a special thank you goes out to the experimental community who have made all their experimental data publicly available however the efforts of many people make this database possible britt park 4state set chen keasar lmds set chris sander misfold set david baker fisa sets enoch huang globins and 4state sets general help jan pedersen general help valuable discussions john moult general help valuable discussions kim simons fisa sets liisa holm misfold set michael levitt globins immunoglobulins and 4state sets general help yu xia lattice_ssfit set references bernstein fc koetzle tf williams gj meyer ej brice md rodgers jr kennard o shimanouchi t tsumi m the protein data bank a computer based archival file for macromolecular structures j mol biol 112 535 542 1977 branden ci jones ta between objectivity and subjectivity nature 343 687 689 1990 fogolari f tosatto sce colombo g a decoy set for the thermostable subdomain from chicken villin headpiece comparison of different free energy estimators bmc bioinformatics 2005 in press halgren ta potential energy functions curr op struct biol 5 205 210 1996 holm l sander c evaluation of protein models by atomic solvation preference cite j mol biol 225 93 105 1992 huang es subbiah s tsai j levitt m using a hydrophobic contact potential to evaluate native and near native folds generated by molecular dynamics simulations j mol biol 257 716 725 1996 keasar c levitt m a novel approach to decoy set generation designing a physical energy function having local minima with native structure characteristics j mol biol 329 159 174 2003 novotny j bruccoleri r karplus m an analysis of incorrectly folded protein models implications for structure predictions j mol biol 177 787 818 1984 park b levitt m energy functions that discriminate x ray and near native folds from well constructed decoys j mol biol 258 367 392 1996 park b huang es levitt m factors affecting the ability of energy functions to discriminate correct from incorrect folds j mol biol 266 831 846 1997 popper kr the logic of scientific discovery new york harper and row 1959 richards f the protein folding problem sci amer 54 63 1991 samudrala r moult j an all atom distance dependent conditional probability discriminatory function for protein structure prediction j mol biol 275 893 914 1998a samudrala r moult j a graph theoretic algorithm for comparative modelling of protein structure j mol biol 279 287 302 1998b samudrala r huang es levitt m selection of the most native like conformations from a set of models constructed by homology modelling in preparation 1998c samudrala r xia y levitt m huang es a combined approach for ab initio construction of low resolution protein tertiary structures from sequence proceedings of the pacific symposium on biocomputing 505 516 1999 samudrala r levitt m a comprehensive analysis of 40 blind protein structure predictions bmc structural biology 2 3 18 2002 simons kt kooperberg c huang es baker d assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions j mol biol 268 209 225 1997 storch em daggett v molecular dynamics of cytochrome b5 implications for protein protein recognition biochemistry 34 9682 9693 subramaniam s tcheng dk fenton jm a knowledge based method for protein structure refinement and prediction in proceedings of the fourth international conference on intelligent systems in molecular biology states d j and agarwal p and gaasterland t and hunter l and smith r f eds 218 229 1996 wang y zhang h scott ra discriminating compact non native structures from the native structure of globular proteins proc nat acad sci usa 92 709 713 1995 xia y huang es levitt m samudrala r ab initio construction of protein tertiary ...