From owner-chemistry@ccl.net Thu Mar 22 05:38:00 2012 From: "liu junjun ljjlp03*o*gmail.com" To: CCL Subject: CCL: about REMD simulation on sugar Message-Id: <-46542-120322011046-11784-Ms/PdcpmMXkvKWOQtTzA7g||server.ccl.net> X-Original-From: liu junjun Content-Type: multipart/alternative; boundary=0016e6de006cf2b63404bbcdd0e4 Date: Thu, 22 Mar 2012 13:02:35 +0800 MIME-Version: 1.0 Sent to CCL by: liu junjun [ljjlp03-,-gmail.com] --0016e6de006cf2b63404bbcdd0e4 Content-Type: text/plain; charset=ISO-8859-1 Hello all, I am trying to simulate a sugar system (disaccharide) to examine its conformation by performing Replica Exchange MD simulation (REMD). I notice that some chirality restraints are required to avoid non-physical chiralities at high temperature in the REMD simulation on peptide, as stated on AMBER tutorial (http://ambermd.org/tutorials/advanced/tutorial7/) My question is, rather than for peptide, are the chirality restraints also required in the REMD simulation on disaccharide? In another word, is it possible that the disaccharide's chiralities change at high temperature? Thanks in advance! Junjun --0016e6de006cf2b63404bbcdd0e4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello all,

= I am trying to simulate a = sugar system (disac= charide) to examine its conformation by performing Replica Exchange MD simu= lation (REMD).=A0I notice that some chirality restr= aints are required to avoid non-physical chiralities at high temperature in= the REMD simulation on peptide, as stated on AMBER tutorial (http://ambermd.org/tutorial= s/advanced/tutorial7/)

My question is, rather than for peptide, are th= e=A0chirality restraints=A0also requ= ired in the REMD simulation on=A0disaccharide? In another word, is it possible that the disaccharide'= ;s chiralities change at high temperature?=A0

Thanks in advance!=

Junjun --0016e6de006cf2b63404bbcdd0e4-- From owner-chemistry@ccl.net Thu Mar 22 07:43:01 2012 From: "Vincent Leroux vincent.leroux=loria.fr" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46543-120322063139-5040-iuDx584H1PjfQPE3ZDf2wA]~[server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 22 Mar 2012 11:31:17 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr] Hi Prija, First, one simple question: do you really need to take into account those multiple crystal structures? If all co-crystallized ligands are found in the exact same binding mode, then, as Vladimir said, all you need is to pick the X-ray structure with the best resolution and use it as reference for your docking studies. The first thing to do is therefore to read carefully all the publications associated to the PDB entries. If you are facing a very flexible receptor that exhibits multiple ligand binding modes when in complex, then you are right to consider using an ensemble of conformations for docking. How to do so is not obvious. You can first filter out the X-ray-derived structures with poor resolution (> 2.5 Ã…), provided they are not showing anything particularly specific compared to the others (if so, some quality checking is advised before use). You can also make sure that the structures are consistent (correct mutants, missing residues, etc.), this is not mandatory for docking but it will be very helpful if you want to go at another level (molecular mechanics). Then you can also set up some MD simulations to explore the receptor conformational space further from what you have from the multiple X-rays. Here is an article that describes different methods that can be used in order to build a relevant ensemble of receptor conformations for docking studies: http://dx.doi.org/10.1002/prot.24021 (you can ask me a copy if you cannot get access to the full text) A clustering program like Wordom may be used you want or need to select a minimal ensemble of conformations for docking. If you have access to GOLD I would recommend its recently-implemented ensemble docking capabilities, very efficient from a computational point of view at the cost of a little higher risk of getting false positives / requires more careful post-docking analysis (no self-reference this time as the paper is not finished yet). Regards VL On 21/03/2012 20:29, Vladimir Chupakhin chupvl,gmail.com wrote: > Hello, > > in my opinion there is no way to choose the "perfect" protein > conformation for ligand-receptor interactoin studies. Choose the protein > with the best quality (<2.5A), and it will be better to dock to every > protein and compare the results. The last one will be the more honest way. > > If you have some quntitative data - activity for example, try to find > correlation between activity and scoring function, the one with the best > correlation is "more" correct protein conformation. > > Best regards, > -- > *Vladimir Chupakhin*, > Independent researcher > in chemoinformatics and structural bioinformatics. > Mobile: +1-617-943-9710 > skype: chupvl > ==-0-0-== > /*Currently looking for job in San Diego area.*/ > > On Wed, Mar 21, 2012 at 12:21, Prija Ponnan prija.ponnan:-:gmail.com > > wrote: > > Hello all > > Its a general query not directly related to Autodock usage.I want to > study interaction of certain coumarin molecules with INHA > > > (Enoyl-[acyl-carrier-protein] reductase [NADH]) of > /Mycobacterium tuberculosis/ > > In PDB database 36 crystal structure entries of this protein is > available.Can anyone please suggest as how should I choose any > one/few crystal structure among them or am I supposed to dock my > compounds with all the available 36 crystal structures of this protein. > > > Thank you > > > Prija Ponnan > PhD Chemistry > University of Delhi > Delhi-110007,India > > > > > > > / > / > From owner-chemistry@ccl.net Thu Mar 22 08:18:01 2012 From: "Krati Joshi kjjulie.joshi~!~gmail.com" To: CCL Subject: CCL:G: Error in gaussian frequency calculation Message-Id: <-46544-120322070532-19391-Aiu6IRbELAkuJ+RLU1Gbfw:server.ccl.net> X-Original-From: "Krati Joshi" Date: Thu, 22 Mar 2012 07:05:30 -0400 Sent to CCL by: "Krati Joshi" [kjjulie.joshi__gmail.com] Dear CCL users, For a long time i am trying to run opt+frq calculation in gaussian (DFT) and everytime when i restart the calculation,first job i.e. optimization terminates normally but frequency terminates with an error message- Error termination in NtrErr: NtrErr called from FIOCnC. I got some solutions from earlier mails sent to CCl but no one worked in my case. My output looks like- %nprocshared=1 Will use up to 1 processors via shared memory. %mem=2500MB %chk=sulcon.chk ----------------------------------- # opt=restart freq b3lyp/6-31g(d,p) ----------------------------------- 99/5=4/99; Restoring state from the checkpoint file "sulcon.chk". Title: sulcon Route: # opt freq b3lyp/6-31g(d,p) I WANT TO KNOW HOW GOD CREATED THE WORLD. I AM NOT INTERESTED IN THIS OR THAT PHENOMENON, IN THE SPECTRUM OF THIS OR THAT ELEMENT. I WANT TO KNOW HIS THOUGHTS, THE REST ARE DETAILS. -- ALBERT EINSTEIN Job cpu time: 0 days 0 hours 0 minutes 0.5 seconds. File lengths (MBytes): RWF= 71 Int= 0 D2E= 0 Chk= 98 Scr= 1 Normal termination of Gaussian 09 at Fri Mar 16 14:03:11 2012. Link1: Proceeding to internal job step number 2. ---------------------------------------------------------------------- #N Geom=AllCheck Guess=TCheck SCRF=Check GenChk RB3LYP/6-31G(d,p) Freq ---------------------------------------------------------------------- 1/10=4,29=7,30=1,38=1,40=1/1,3; 2/12=2,40=1/2; 3/5=1,6=6,7=101,11=2,14=-4,16=1,25=1,30=1,70=2,71=2,74=-5,116=1/1,2,3; 4/5=101/1; 5/5=2,98=1/2; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 7/8=1,10=1,25=1/1,2,3,16; 1/10=4,30=1/3; 99//99; ------ sulcon ------ Redundant internal coordinates taken from checkpoint file: sulcon.chk Charge = 0 Multiplicity = 1 S,0,-0.1083680207,0.0288457269,0.0247583371 O,0,-0.1961903903,-0.0073508404,1.4840514917 O,0,1.1613958515,0.053027157,-0.6838258851 O,0,-0.9336947234,-1.2783333555,-0.5318824828 H,0,-1.3158237177,-1.7253654694,0.2432009386 C,0,-1.1095870324,1.3774380987,-0.5787114899 C,0,-0.8401063721,1.9263765465,-1.8278448331 C,0,-1.6269139928,2.9676068255,-2.3247354223 C,0,-2.7029378412,3.428893397,-1.5416405559 C,0,-2.9710048708,2.8864981118,-0.2719477711 C,0,-2.1537047901,1.8621453851,0.2035480497 O,0,-3.5604258028,4.4165346833,-1.96974758 H,0,-3.2226795881,4.9195223101,-2.7328995938 H,0,-0.0080760942,1.5443127428,-2.4096760314 H,0,-2.3166875127,1.4494888543,1.1935632206 C,0,-1.278541325,3.5820221122,-3.6703164914 H,0,-2.1829687921,3.6947593552,-4.277166819 H,0,-0.6423313547,2.877318983,-4.2126889985 C,0,-0.5371073098,4.907892529,-3.5492025722 C,0,-1.1608347114,6.1355361564,-3.8032508854 C,0,1.4680010892,6.1426666646,-3.0362419226 O,0,-2.5336457266,6.134017588,-4.1370919722 H,0,-2.6556397039,5.7247126387,-5.007404771 H,0,1.337471592,4.0005637359,-2.9671039553 H,0,1.3985646269,8.2777149013,-3.2483639872 S,0,3.1918758296,6.1515090037,-2.5463931448 O,0,3.7907965106,7.421158106,-2.9546445524 O,0,3.7667444737,4.8659561633,-2.9073034178 O,0,3.0585238126,6.187102355,-0.9124493291 C,0,-0.5054117319,7.3710223989,-3.7049522688 C,0,0.8061502548,4.9260668252,-3.1620266528 C,0,0.8352654745,7.3527259695,-3.3103766088 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! -------------------------- -------------------------- ! Name Definition Value Derivative Info. ! -------------------------------------------------------------------------------- ! R1 R(1,2) 1.4624 calculate D2E/DX2 analytically ! ! R2 R(1,3) 1.4543 calculate D2E/DX2 analytically ! ! R3 R(1,4) 1.6431 calculate D2E/DX2 analytically ! ! R4 R(1,6) 1.7847 calculate D2E/DX2 analytically ! ! R5 R(4,5) 0.9729 calculate D2E/DX2 analytically ! ! R6 R(6,7) 1.3908 calculate D2E/DX2 analytically ! ! R7 R(6,11) 1.3918 calculate D2E/DX2 analytically ! ! R8 R(7,8) 1.3965 calculate D2E/DX2 analytically ! ! R9 R(7,14) 1.0848 calculate D2E/DX2 analytically ! ! R10 R(8,9) 1.4085 calculate D2E/DX2 analytically ! ! R11 R(8,16) 1.5197 calculate D2E/DX2 analytically ! ! R12 R(9,10) 1.4065 calculate D2E/DX2 analytically ! ! R13 R(9,12) 1.3762 calculate D2E/DX2 analytically ! ! R14 R(10,11) 1.394 calculate D2E/DX2 analytically ! ! R15 R(10,34) 1.5172 calculate D2E/DX2 analytically ! ! R16 R(11,15) 1.0849 calculate D2E/DX2 analytically ! ! R17 R(12,13) 0.9744 calculate D2E/DX2 analytically ! ! R18 R(12,44) 1.9049 calculate D2E/DX2 analytically ! ! R19 R(13,25) 1.9803 calculate D2E/DX2 analytically ! ! R20 R(16,17) 1.095 calculate D2E/DX2 analytically ! ! R21 R(16,18) 1.0934 calculate D2E/DX2 analytically ! ! R22 R(16,19) 1.5239 calculate D2E/DX2 analytically ! ! R23 R(19,20) 1.4002 calculate D2E/DX2 analytically ! ! R24 R(19,22) 1.3981 calculate D2E/DX2 analytically ! ! R25 R(20,21) 1.402 calculate D2E/DX2 analytically ! ......................... ............... ....... and so on..... Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 Number of steps in this run= 2 maximum allowed number of steps= 2. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Stoichiometry C42H36O24S6 Framework group C1[X(C42H36O24S6)] Deg. of freedom 318 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 16 0 -1.795959 6.525253 1.400341 2 8 0 -1.246900 6.423549 2.751914 3 8 0 -3.148894 6.988937 1.136633 ................. ............. ...............so on Rotational constants (GHZ): 0.0274482 0.0187940 0.0130241 Standard basis: 6-31G(d,p) (6D, 7F) There are 1284 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 1284 basis functions, 2412 primitive gaussians, 1284 cartesian basis functions 288 alpha electrons 288 beta electrons nuclear repulsion energy 14205.2093828915 Hartrees. NAtoms= 108 NActive= 108 NUniq= 108 SFac= 1.00D+00 NAtFMM= 50 NAOKFM=T Big=T One-electron integrals computed using PRISM. NBasis= 1284 RedAO= T NBF= 1284 NBsUse= 1284 1.00D-06 NBFU= 1284 SCF restart from the checkpoint file: sulcon.chk B after Tr= 0.000000 0.000000 0.000000 Rot= 1.000000 0.000000 0.000000 0.000000 Ang= 0.00 deg. Initial guess orbital symmetries: Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) .............................. . ..................................... Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. SCF Done: E(RB3LYP) = -5816.36813833 A.U. after 3 cycles Convg = 0.1015D-08 -V/T = 2.0069 Range of M.O.s used for correlation: 1 1284 NBasis= 1284 NAE= 288 NBE= 288 NFC= 0 NFV= 0 NROrb= 1284 NOA= 288 NOB= 288 NVA= 996 NVB= 996 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 55 centers at a time, making 2 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through L=2. End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 327 degrees of freedom in the 1st order CPHF. IDoFFX=5. Internal consistency error detected in FileIO for unit 1 I= 7 J= 0 IFail= 1. dumping /fiocom/, unit = 1 NFiles = 89 SizExt = 262144 WInBlk = 4096 defal = F LstWrd = -1756700672 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 501 Number 0 0 0 0 0 0 0 501 Base 17183175 12607488 39055360 15917056 21712896 16752640-1756965376 45056 End 17571840 12611584 109178880 15921152 26664960 16756736-1756700672 46056 End1 17571840 12611584 109178880 15921152 26664960 16756736-1756700672 49152 Wr Pntr 16896000 12607488 39055360 15917056 21712896 16752640 662016000 45056 Rd Pntr 16896000 12607488 39055360 15917056 21712896 16752640 662016000 45056 Length 388665 4096 70123520 4096 4952064 4096 264704 1000 Number 502 503 507 508 511 514 515 516 Base 73728 135168 143360 761856 512000 6582272 3280896 802816 End 77707 135871 144283 761871 688716 7407242 6580776 3277726 End1 77824 139264 147456 765952 692224 7409664 6582272 3280896 Wr Pntr 73728 135168 143360 761856 512000 6582272 3280896 802816 Rd Pntr 73728 135168 143360 761856 512000 6582272 3280896 802816 Length 3979 703 923 15 176716 824970 3299880 2474910 Number 517 518 520 521 522 523 524 526 Base 12468224 9990144 790528 720896 16748544 14262272 12611584 14266368 End 12606896 12465054 790533 720931 16751112 14264840 14260240 15915024 End1 12607488 12468224 794624 724992 16752640 14266368 14262272 15917056 Wr Pntr 12468224 9990144 790528 720896 16748544 14262272 12611584 14266368 Rd Pntr 12468224 9990144 790528 720896 16748544 14262272 12611584 14266368 Length 138672 2474910 5 35 2568 2568 1648656 1648656 Number 528 530 532 534 536 538 545 547 Base 17571840 15921152 18403328 19230720 20058112 20885504 16764928 16773120 End 18396810 16746122 19228298 20055690 20883082 21710474 16764942 16775688 End1 18399232 16748544 19230720 20058112 20885504 21712896 16769024 16777216 Wr Pntr 17571840 15921152 18403328 19230720 20058112 20885504 16764928 16773120 Rd Pntr 17571840 15921152 18403328 19230720 20058112 20885504 16764928 16773120 Length 824970 824970 824970 824970 824970 824970 14 2568 Number 548 551 552 559 562 563 565 569 Number 548 551 552 559 562 563 565 569 Number 994 995 996 997 998 999 2999 3001 Base 20480 36864 28672 32768 24576 81920 16781312 380608512 End 20510 36874 28772 34281 24776 133172 16888241 474407808 End1 24576 40960 32768 36864 28672 135168 16891904 474411008 Wr Pntr 20480 36864 28672 32768 24576 81920 16781312 380608512 Rd Pntr 20480 36864 28672 32768 24576 81920 16781312 380608512 Length 30 10 100 1513 200 51252 106929 93799296 Number 3003 3005 3007 3026 9995 9996 9997 9998 Base 474411008 34099200 36577280 33271808 1600008960 662016000 16896000 568213504 End 568210304 36574110 39052190 34096778-1756965376 1600008960 17183175 662012800 End1 568213504 36577280 39055360 34099200-1756965376 1600008960 17183175 662016000 Wr Pntr 474411008 34099200 36577280 33271808 1600008960 662016000 16896000 568213504 Rd Pntr 474411008 34099200 36577280 33271808 1600008960 6620160Number 9999 Base 31621120 End 33271060 End1 33271808 Wr Pntr 31621120 Rd Pntr 31621120 Length 1649940 dumping /fiocom/, unit = 2 NFiles = 37 SizExt = 0 WInBlk = 4096 defal = F LstWrd = 12718080 FType=2 FMxFil=10000 Number 0 0 0 0 0 501 502 503 Base 7337151 7337040 10245164 23263 12715330 3332750 3333750 8163061 End 8162120 7337042 11890359 1682810 12718080 3333750 3337729 8163764 End1 8162120 7337042 11890359 1682810 12718080 3333750 3337729 8163764 Wr Pntr 7337151 7337040 10245164 23263 12715330 3332750 3333750 8163061 Rd Pntr 7337151 7337040 10245164 23263 12715330 3332750 3333750 8163061 Length 824969 2 1645195 1659547 2750 1000 3979 703 Number 508 511 520 521 522 524 526 536 Base 20480 3344531 3549288 4024088 20695 4024123 5672779 1682810 End 20495 3521247 3549293 4024123 23263 5672779 7321435 2507780 End1 20495 3521247 3549293 4024123 23263 5672779 7321435 2507780 Wr Pntr 20480 3344531 3549288 4024088 20695 4024123 5672779 1682810 00 16896000 568213504 Number 538 551 552 562 575 584 603 605 Base 2507780 3549311 3549293 3543241 3549336 3525104 11890359 7337042 End 3332750 3549336 3549311 3549288 4024088 3525752 12715330 7337151 End1 3332750 3549336 3549311 3549288 4024088 3525752 12715330 7337151 Wr Pntr 2507780 3549311 3549293 3543241 3549336 3525104 11890359 7337042 Rd Pntr 2507780 3549311 3549293 3543241 3549336 3525104 11890359 7337042 Length 824970 25 18 6047 474752 648 824971 109 Number 619 634 665 670 672 674 695 698 Base 7321435 8585617 3521247 3337729 8162120 8162289 3525752 8163764 End 7337040 10245164 3525104 3344531 8162289 8163061 3529128 8164412 End1 7337040 10245164 3525104 3344531 8162289 8163061 3529128 8164412 Wr Pntr 7321435 8585617 3521247 3337729 8162120 8162289 3525752 8163764 Rd Pntr 7321435 8585617 3521247 3337729 8162120 8162289 3525752 8163764 Length 15605 1659547 3857 6802 169 772 3376 648 Number 701 989 993 997 998 Base 8164412 3529128 3541628 3541728 20495 End 8585617 3541628 3541728 3543241 20695 End1 8585617 3541628 3541728 3543241 20695 Wr Pntr 8164412 3529128 3541628 3541728 20495 Rd Pntr 8164412 3529128 3541628 3541728 20495 Length 421205 12500 100 1513 200 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 4096 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Length 45056 Error termination in NtrErr: NtrErr called from FIOCnC. Can anybody suggest me how to solve this problem. It will be very helpfull Thanks in advance > From Krati Joshi catalysis division National chemical laboratory Pashan road, pune Email-kjjulie.joshi-at-gmail.com From owner-chemistry@ccl.net Thu Mar 22 10:54:01 2012 From: "Emmanuel Baribefe Naziga baribefe=-=gmail.com" To: CCL Subject: CCL: about REMD simulation on sugar Message-Id: <-46545-120322105239-13725-o6QdU0kPSCDdHYuddmRVVA^server.ccl.net> X-Original-From: Emmanuel Baribefe Naziga Content-Type: multipart/alternative; boundary=20cf303f6d54e21dc104bbd60e34 Date: Thu, 22 Mar 2012 08:52:33 -0600 MIME-Version: 1.0 Sent to CCL by: Emmanuel Baribefe Naziga [baribefe[a]gmail.com] --20cf303f6d54e21dc104bbd60e34 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello, I would say it depends on how high your simulation temperature is, see Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence Tongye Shen,=E2=80=A0,=E2=80=A1 Paul Langan,=C2=A7 Alfred D. French,=E2=8A= =A5 Glenn P. Johnson,=E2=8A=A5 and S. Gnanakaran*,=E2=80=A0 Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, J. AM. CHEM. SOC. 2009, 131, 14786=E2=80=9314794 Cheers Emmanuel On Wed, Mar 21, 2012 at 11:02 PM, liu junjun ljjlp03*o*gmail.com < owner-chemistry!^!ccl.net> wrote: > Hello all, > > I am trying to simulate a sugar system (disaccharide) to examine its > conformation by performing Replica Exchange MD simulation (REMD). I > notice that some chirality restraints are required to avoid non-physical > chiralities at high temperature in the REMD simulation on peptide, as > stated on AMBER tutorial (http://ambermd.org/tutorials/advanced/tutorial7= / > ) > > My question is, rather than for peptide, are the chirality > restraints also required in the REMD simulation on disaccharide? In > another word, is it possible that the disaccharide's chiralities change a= t > high temperature? > > Thanks in advance! > > Junjun > --20cf303f6d54e21dc104bbd60e34 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello,

I would say it depends on how high your simulatio= n temperature is, see

Conformational Flexibil= ity of Soluble Cellulose Oligomers:
Chain Length and Temperature = Dependence
Tongye Shen,=E2=80=A0,=E2=80=A1 Paul Langan,=C2=A7 Alfred D. French,= =E2=8A=A5 Glenn P. Johnson,=E2=8A=A5 and
S. Gnanakaran*,=E2=80=A0=
Theoretical Biology & Biophysics Group, Center for Nonlinear= Studies, and Biosciences,

J. AM. CHEM. SOC. 2009, 131, 14786=E2=80=9314794

<= div>
Cheers

Emmanuel

On Wed, Mar 21, 2012 at 11:02 PM, liu junjun ljjlp03*o= *gmail.com <owner-chemistry!^!ccl.net> = wrote:
Hello all,

I am trying t= o simulate a sugar system (disaccharide) to examine its conformation by perform= ing Replica Exchange MD simulation (REMD).=C2=A0= I notice that some chirality restraints are required to avoid non-phy= sical chiralities at high temperature in the REMD simulation on peptide, as= stated on AMBER tutorial (http://ambermd.org/tutorials/advanced/tutori= al7/)

My question is, rather tha= n for peptide, are the=C2=A0chirality restraints=C2=A0also required i= n the REMD simulation on=C2=A0disaccharide? In another word, i= s it possible that the disaccharide's chiralities change at high temper= ature?=C2=A0

Th= anks in advance!

Ju= njun

--20cf303f6d54e21dc104bbd60e34-- From owner-chemistry@ccl.net Thu Mar 22 12:14:00 2012 From: "Dr. Vitaly V. Chaban vvchaban..gmail.com" To: CCL Subject: CCL:G: "Not enough space in DoHrmC" Message-Id: <-46546-120322121304-11031-DOdPtMNg4UTE9qECz8C22w*o*server.ccl.net> X-Original-From: "Dr. Vitaly V. Chaban" Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Mar 2012 12:12:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban(_)gmail.com] Dear All -- What does the Gaussian 09's error "Not enough space in DoHrmC" mean? It is DFT calculation of a relatively small non-periodic system, so I would not expect out-of-memory or out-of-disk_space origins. -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA From owner-chemistry@ccl.net Thu Mar 22 12:48:01 2012 From: "Prija Ponnan prija.ponnan++gmail.com" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46547-120322122123-22342-mj8JHQVcTn/Wa/0d9T2G6A###server.ccl.net> X-Original-From: Prija Ponnan Content-Type: multipart/alternative; boundary=f46d04428eacf8330304bbd74bd7 Date: Thu, 22 Mar 2012 21:50:33 +0530 MIME-Version: 1.0 Sent to CCL by: Prija Ponnan [prija.ponnan(a)gmail.com] --f46d04428eacf8330304bbd74bd7 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Vincent Thank you for your valuable inputs. It would have been great if you could send a copy of your paper as I am unable to get access to it. Prija On Thu, Mar 22, 2012 at 4:01 PM, Vincent Leroux vincent.leroux=3Dloria.fr < owner-chemistry-x-ccl.net> wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr] > Hi Prija, > > First, one simple question: do you really need to take into account those > multiple crystal structures? If all co-crystallized ligands are found in > the exact same binding mode, then, as Vladimir said, all you need is to > pick the X-ray structure with the best resolution and use it as reference > for your docking studies. The first thing to do is therefore to read > carefully all the publications associated to the PDB entries. > > If you are facing a very flexible receptor that exhibits multiple ligand > binding modes when in complex, then you are right to consider using an > ensemble of conformations for docking. How to do so is not obvious. You c= an > first filter out the X-ray-derived structures with poor resolution (> 2.5 > =C5), provided they are not showing anything particularly specific compar= ed > to the others (if so, some quality checking is advised before use). You c= an > also make sure that the structures are consistent (correct mutants, missi= ng > residues, etc.), this is not mandatory for docking but it will be very > helpful if you want to go at another level (molecular mechanics). Then yo= u > can also set up some MD simulations to explore the receptor conformationa= l > space further from what you have from the multiple X-rays. > > Here is an article that describes different methods that can be used in > order to build a relevant ensemble of receptor conformations for docking > studies: http://dx.doi.org/10.1002/**prot.24021 > (you can ask me a copy if you cannot get access to the full text) > > A clustering program like Wordom may be used you want or need to select a > minimal ensemble of conformations for docking. If you have access to GOLD= I > would recommend its recently-implemented ensemble docking capabilities, > very efficient from a computational point of view at the cost of a little > higher risk of getting false positives / requires more careful post-docki= ng > analysis (no self-reference this time as the paper is not finished yet). > > Regards > VL > > > On 21/03/2012 20:29, Vladimir Chupakhin chupvl,gmail.com wrote: > >> Hello, >> >> in my opinion there is no way to choose the "perfect" protein >> conformation for ligand-receptor interactoin studies. Choose the protein >> with the best quality (<2.5A), and it will be better to dock to every >> protein and compare the results. The last one will be the more honest wa= y. >> >> If you have some quntitative data - activity for example, try to find >> correlation between activity and scoring function, the one with the best >> correlation is "more" correct protein conformation. >> >> Best regards, >> -- >> *Vladimir Chupakhin*, >> Independent researcher >> in chemoinformatics and structural bioinformatics. >> Mobile: +1-617-943-9710 >> skype: chupvl >> =3D=3D-0-0-=3D=3D >> /*Currently looking for job in San Diego area.*/ >> >> On Wed, Mar 21, 2012 at 12:21, Prija Ponnan prija.ponnan:-:gmail.com >> > >> wrote: >> >> Hello all >> >> Its a general query not directly related to Autodock usage.I want to >> study interaction of certain coumarin molecules with INHA >> >> >> (Enoyl-[acyl-carrier-protein] reductase [NADH]) of >> /Mycobacterium tuberculosis/ >> >> In PDB database 36 crystal structure entries of this protein is >> available.Can anyone please suggest as how should I choose any >> one/few crystal structure among them or am I supposed to dock my >> compounds with all the available 36 crystal structures of this protei= n. >> >> >> Thank you >> >> >> Prija Ponnan >> PhD Chemistry >> University of Delhi >> Delhi-110007,India >> >> >> >> >> >> >> / >> / >> >> > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --f46d04428eacf8330304bbd74bd7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Vincent

Thank you for your valuable inputs. It would have been gr= eat if you could send a copy of your paper as I am unable to get access to = it.


Prija=A0
=A0



On Thu, Mar 22, 2012 at 4:01 PM, Vincent= Leroux vincent.leroux=3Dloria.fr <owner-chemistry-x-ccl= .net> wrote:

Sent to CCL by: Vincent Leroux [vincent.leroux+*+loria.fr]
Hi Prija,

First, one simple question: do you really need to take into account those m= ultiple crystal structures? If all co-crystallized ligands are found in the= exact same binding mode, then, as Vladimir said, all you need is to pick t= he X-ray structure with the best resolution and use it as reference for you= r docking studies. The first thing to do is therefore to read carefully all= the publications associated to the PDB entries.

If you are facing a very flexible receptor that exhibits multiple ligand bi= nding modes when in complex, then you are right to consider using an ensemb= le of conformations for docking. How to do so is not obvious. You can first= filter out the X-ray-derived structures with poor resolution (> 2.5 =C5= ), provided they are not showing anything particularly specific compared to= the others (if so, some quality checking is advised before use). You can a= lso make sure that the structures are consistent (correct mutants, missing = residues, etc.), this is not mandatory for docking but it will be very help= ful if you want to go at another level (molecular mechanics). Then you can = also set up some MD simulations to explore the receptor conformational spac= e further from what you have from the multiple X-rays.

Here is an article that describes different methods that can be used in ord= er to build a relevant ensemble of receptor conformations for docking studi= es: http= ://dx.doi.org/10.1002/prot.24021
(you can ask me a copy if you cannot get access to the full text)

A clustering program like Wordom may be used you want or need to select a m= inimal ensemble of conformations for docking. If you have access to GOLD I = would recommend its recently-implemented ensemble docking capabilities, ver= y efficient from a computational point of view at the cost of a little high= er risk of getting false positives / requires more careful post-docking ana= lysis (no self-reference this time as the paper is not finished yet).

Regards
VL


On 21/03/2012 20:29, Vladimir Chupakhin chupvl,gmail.com wrote:
Hello,

in my opinion there is no way to choose the "perfect" protein
conformation for ligand-receptor interactoin studies. Choose the protein with the best quality (<2.5A), and it will be better to dock to every protein and compare the results. The last one will be the more honest way.<= br>
If you have some quntitative data - activity for example, try to find
correlation between activity and scoring function, the one with the best correlation is "more" correct protein conformation.

Best regards,
--
*Vladimir Chupakhin*,
Independent researcher
in chemoinformatics and structural bioinformatics.
Mobile: +1-617-943-9710
skype: chupvl
=3D=3D-0-0-=3D=3D
/*Currently looking for job in San Diego area.*/

On Wed, Mar 21, 2012 at 12:21, Prija Ponnan prija.ponnan:-:gmail.com
<http://gmail.com>= <owner-chemistry+/-ccl.net=
<mailto:owner-ch= emistry+/-ccl.net>> wrote:

=A0 =A0Hello all

=A0 =A0Its a general query not directly related to Autodock usage.I want t= o
=A0 =A0study interaction of certain coumarin molecules with INHA


=A0 =A0 =A0 =A0 =A0(Enoyl-[acyl-carrier-protein] reductase [NADH]) of
=A0 =A0 =A0 =A0 =A0/Mycobacterium tuberculosis/

=A0 =A0In PDB database 36 crystal structure entries of this protein is
=A0 =A0available.Can anyone please suggest as how should I choose any
=A0 =A0one/few crystal structure among them or am I supposed to dock my =A0 =A0compounds with all the available 36 crystal structures of this prot= ein.


=A0 =A0Thank you


=A0 =A0Prija Ponnan
=A0 =A0PhD Chemistry
=A0 =A0University of Delhi
=A0 =A0Delhi-110007,India






/
/




-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY-x-ccl.net or use:
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--f46d04428eacf8330304bbd74bd7-- From owner-chemistry@ccl.net Thu Mar 22 15:02:00 2012 From: "Bradley Welch bwelch5_._slu.edu" To: CCL Subject: CCL: Simple Matlab Question Message-Id: <-46548-120322150100-616-hnIkpUqygxwW/i6XGG5qGg],[server.ccl.net> X-Original-From: "Bradley Welch" Date: Thu, 22 Mar 2012 15:00:57 -0400 Sent to CCL by: "Bradley Welch" [bwelch5- -slu.edu] Dear all, I have a simple matlab question that will probably get me laughed at. I'm using the curve fitting tool function (cftool for short). I have my curve and the graph. My question is how do I export this graph to say word or open office? My graphs look very nice and I want to use them for my poster at an upcoming local conference. Thank you, Bradley Welch Saint Louis University From owner-chemistry@ccl.net Thu Mar 22 15:45:01 2012 From: "uekstrom|,|gmail.com uekstrom|,|gmail.com" To: CCL Subject: CCL: Simple Matlab Question Message-Id: <-46549-120322154312-14193-znYSo5wNpuANLnMbFF9RLA]=[server.ccl.net> X-Original-From: "uekstrom : gmail.com" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Mar 2012 20:43:05 +0100 MIME-Version: 1.0 Sent to CCL by: "uekstrom-.-gmail.com" [uekstrom-.-gmail.com] > I'm using the curve fitting tool function (cftool for short). I have my curve and the graph. My question is how do I export this graph to say word or open office? My graphs look very nice and I want to use them for my poster at an upcoming local conference. Ok, so there is this website called google.com. If I write "matlab save figure" into it I get the correct answer _as the first hit_. Maybe try that? Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Thu Mar 22 16:20:00 2012 From: "Pedro Silva pedros===ufp.edu.pt" To: CCL Subject: CCL: Simple Matlab Question Message-Id: <-46550-120322161349-25960-iqgVrjHLQolQb+nYzlVZIg:server.ccl.net> X-Original-From: Pedro Silva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Mar 2012 20:13:42 +0000 MIME-Version: 1.0 Sent to CCL by: Pedro Silva [pedros-#-ufp.edu.pt] I would simply do a print screen and paste it into my favorite graphic software :-) Pedro On Thu, Mar 22, 2012 at 7:00 PM, Bradley Welch bwelch5_._slu.edu wrote: > > Sent to CCL by: "Bradley   Welch" [bwelch5- -slu.edu] > Dear all, > > I have a simple matlab question that will probably get me laughed at. > > I'm using the curve fitting tool function (cftool for short). I have my curve and the graph. My question is how do I export this graph to say word or open office? My graphs look very nice and I want to use them for my poster at an upcoming local conference. > > Thank you, > > Bradley Welch > Saint Louis University>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > -- Pedro J. Silva Associate Professor Universidade Fernando Pessoa Porto - Portugal http://homepage.ufp.pt/pedros/science/science.htm http://biochemicalmatters.blogspot.com From owner-chemistry@ccl.net Thu Mar 22 17:38:00 2012 From: "Maurizio Bronzetti mauriziospacezero-ccl/./yahoo.com" To: CCL Subject: CCL: Mobile Chemistry: SPRESImobile app for iPhone and iPad Message-Id: <-46551-120322173230-10236-7zxWW4preL+cmKa36ykqBw::server.ccl.net> X-Original-From: Maurizio Bronzetti Content-Type: multipart/alternative; boundary="-337026386-1445530493-1332451941=:72182" Date: Thu, 22 Mar 2012 14:32:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Maurizio Bronzetti [mauriziospacezero-ccl . yahoo.com] ---337026386-1445530493-1332451941=:72182 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello all,=A0=0A=0AInfoChem (http://infochem.de) recently released a free m= obile app for iPhone and iPad that gives access to over 410k+ reactions. I = believe the app is noteworthy for the innovative interface and workflow nav= igation. To the best of my knowledge, =A0it is also the first iPad/iPhone c= hemistry app that enables users to go through a complete search/browse-resu= lts-and-references-workflow that includes "live" molecules and reactions. Y= ou can also share mol and rxn files via emails with colleagues or friends.= =A0=0A=0AThe app was developed in collaboration w/Eidogen-Sertanty (http://= eidogen-sertanty.com) and uses an embedded version of the MMDS by Molecular= Materials Informatics (http://molmatinf.com)=A0 as native drawing editor. = =A0 =A0=0A=0AI suggest to check out the SPRESImobile page at=A0http://infoc= hem.de/products/databases/spresimobile.shtml=0A=0AAlso, If you are interest= ed in learning more, the app will be launched at the ACS and my understandi= ng is that InfoChem will showcase it at their booth and during the CINF rec= eption this Sunday.=A0=0AThanks,=0A=0A=A0Maurizio Bronzetti.=0A ---337026386-1445530493-1332451941=:72182 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello all, = ;

InfoChem (http://infoc= hem.de) recently released a free mobile app for iPhone and iPad = that gives access to over 410k+ reactions. I believe the app is noteworthy = for the innovative interface and workflow navigation. To the best of my kno= wledge,  it is also the first iPad/iPhone chemistry app that enables users to= go through a complete search/browse-results-and-references-workflow that i= ncludes "live" molecules and reactions. You can also share mol and rxn file= s via emails with colleagues or friends. 

The= app was developed in collaboration w/Eidogen-Sertanty (http://eidogen-sertanty.com) and uses an embedde= d version of the MMDS by Molecular Materials Informatics (http://molmatinf.com)  as native drawing editor.  =  

I suggest to check out the SPRESImobile pa= ge at http://infochem.de/products/databases/spresimobile.= shtml

Also, If you are intereste= d in learning more, the app will be launched at the ACS and my understanding is that InfoChem = will showcase it at their booth and during the CINF reception this Sunday.&= nbsp;

Thanks,

=
 Maurizio Bronzetti.<= /span>

---337026386-1445530493-1332451941=:72182-- From owner-chemistry@ccl.net Thu Mar 22 18:13:00 2012 From: "Greg Warren greg%a%eyesopen.com" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46552-120322132321-27787-Cm8e+CG48w7nrJaEuJP3jg#,#server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BB3CCF2D3D6B094D96588383620C5F3EADADCE549DEXVMBX01811ex_" Date: Thu, 22 Mar 2012 10:23:07 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg,+,eyesopen.com] --_000_BB3CCF2D3D6B094D96588383620C5F3EADADCE549DEXVMBX01811ex_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Prija, There are methods or criteria you can use to select the highest quality st= ructure - the structure with the lowest noise or model error. The resolu= tion the structure was solved at is probably one of the poorest methods for= selecting. If the 36 structures you are attempting to select from have ha= d structure factors deposited then you can access more robust selection met= rics using the EDS web site (http://eds.bmc.uu.se/eds/). The metric I find the most robust and = intuitively useful is density precision index (DPI). You can think of this= metric as similar to the coordinate error for the structure. The lower th= e coordinate error (DPI) the better the structure. The value is found as "= Cruickshank DPI" on the EDS summary page for the structure. The previous paragraph is about how to select the highest quality structure= which may or may not be the best structure for your docking studies. Be= cause you are planning on docking coumarin derivatives into your TB target = my guess is that the chemical diversity of your molecules is not large. Th= ere was a publication on cross docking which included results for AutoDock = 4 in 2010 that addresses your problem. The reference is J. Chem. Inf. Mod= el. 50, 1432 (2010). This study showed that for cross-docking (the exper= iment you are planning on doing) success is strongly related to the similar= ity between the molecule being docked and the ligand in the protein-ligand = complex structure. They used a 3-D shape comparison metric from OpenEye (T= animotoCombo) but you could also use 2-D similarity methods. To quickly summarize, there are a number of robust methods that can be used= to select the highest quality structure but the resolution of the structur= e is not one of them. I would recommend using DPI. In your case, if there= are a number of structures with a similar DPI values (<0.3) then the struc= ture you should use is the one with a ligand that is the most similar to th= e ligands you are docking (using a 2-D or 3-D similarity metric). There are, of course, more complicated ways to approach the problem you hav= e. From my reading of the literature it is not clear to me that these meth= ods provide a clear added value when one considers the cost of using and in= terpreting the data from the more complicated methods. Regards, Greg =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Gregory Warren, PhD Senior Applications Scientist CEAPAS OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg:_:eyesopen.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > From: owner-chemistry+greg=3D=3Deyesopen.com:_:ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com:_:ccl.net] On Behalf Of Prija Ponnan prija.ponnan:-:= gmail.com Sent: Wednesday, March 21, 2012 10:21 AM To: Greg Warren Subject: CCL: Docking studies with multiple crystal structures of a protein Hello all Its a general query not directly related to Autodock usage.I want to study = interaction of certain coumarin molecules with INHA (Enoyl-[acyl-carrier-protein] reductase [NADH]) of Mycobacterium tuberculos= is In PDB database 36 crystal structure entries of this protein is available.C= an anyone please suggest as how should I choose any one/few crystal structu= re among them or am I supposed to dock my compounds with all the available = 36 crystal structures of this protein. Thank you Prija Ponnan PhD Chemistry University of Delhi Delhi-110007,India --_000_BB3CCF2D3D6B094D96588383620C5F3EADADCE549DEXVMBX01811ex_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Prij= a,

 

There are methods or criteria you can use = to select the highest quality  structure - the structure with the lowe= st noise or model error.    The resolution the structure was= solved at is probably one of the poorest methods for selecting.  If t= he 36 structures you are attempting to select from have had structure facto= rs deposited then you can access more robust selection metrics using the ED= S web site (http://eds.bmc.uu.se/eds<= /a>/).  The metric I find th= e most robust and intuitively useful is density precision index (DPI). = ; You can think of this metric as similar to the coordinate error for the s= tructure.  The lower the coordinate error (DPI) the better the structu= re.  The value is found as “Cruickshank DPI” on the EDS su= mmary page for the structure.

 

The previous pa= ragraph is about how to select the highest quality structure which may or m= ay not be the best structure for your docking studies.    Be= cause you are planning on docking coumarin derivatives into your TB target = my guess is that the chemical diversity of your molecules is not large.&nbs= p; There was a publication on cross docking which included results for Auto= Dock 4 in 2010 that addresses your problem.  The reference is  J. Chem. Inf. Model. 50, 1432 (2010).   This study sh= owed that  for cross-docking (the experiment you are planning on doing= ) success is strongly related to the similarity between the molecule being = docked and the ligand in the protein-ligand complex structure.  They u= sed a 3-D shape comparison metric from OpenEye (TanimotoCombo) but you coul= d also use 2-D similarity methods.

 

To quickly= summarize, there are a number of robust methods that can be used to select= the highest quality structure but the resolution of the structure is not o= ne of them.  I would recommend using DPI.  In your case, if there= are a number of structures with a similar DPI values (<0.3) then the st= ructure you should use is the one with a ligand that is the most similar to= the ligands you are docking (using a 2-D or 3-D similarity metric).

 

There are, of course, more complicated ways to appr= oach the problem you have.  From my reading of the literature it is no= t clear to me that these methods provide a clear added value when one consi= ders the cost of using and interpreting the data from the more complicated = methods.

 =

Regards,

 

Greg

 <= /span>

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D

Gregory Warren, = PhD

Senior Applications Sc= ientist

CEAPAS<= /span>

OpenEye Scientific Software, Inc=

9 Bisbee Court, Suite D

Santa Fe, NM 87508

(505) 473-7385 ext 50=

mailto:greg:_:eyesopen.com<= /p>

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D

 

 

 

 

From: owner-chemistry+greg=3D=3D= eyesopen.com:_:ccl.net [mailto:owner-chemistry+greg=3D=3Deyesopen.com:_:ccl.net= ] On Behalf Of Prija Ponnan prija.ponnan:-:gmail.com
Sent:= Wednesday, March 21, 2012 10:21 AM
To: Greg Warren
Subject= : CCL: Docking studies with multiple crystal structures of a protein

 

Hello all

Its a general query not directly related to Autodock usage.= I want to study interaction of certain coumarin molecules with INHA

(Enoyl-[acy= l-carrier-protein] reductase [NADH]) of Mycobacterium tuberculosis

In PDB database 36 crystal structure entries of thi= s protein is available.Can anyone please suggest as how should I choose any= one/few crystal structure among them or am I supposed to dock my compounds= with all the available 36 crystal structures of this protein.

 

Thank you


Prija Ponnan
PhD Chemistry=
University of Delhi
Delhi-110007,India

 

 

= --_000_BB3CCF2D3D6B094D96588383620C5F3EADADCE549DEXVMBX01811ex_--