Modeller_Usage Mailing List (by thread)
- [modeller_usage] Problems about disulfide bonds,
饶?
- [modeller_usage] modeller model and modbase model,
hori koshii
- [modeller_usage] Ligands,
Joel Tyndall
- [modeller_usage] origin of blosum62.sim.mat and as1.sim.mat,
Joshua A. Speidel
- [modeller_usage] Cómo instalar MODELLER,
Carlos Lozano
- [modeller_usage] forrtl Error using the "/." construct,
Schmid, Dr R.
- [modeller_usage] (no subject),
Purzelfrau
- [modeller_usage] help about evaluate_model.log,
Purzelfrau
- [modeller_usage] Modeller 9v1 release,
Modeller Caretaker
- [modeller_usage] using restraints from saxs data,
Christian Meesters
- [modeller_usage] Model evaluation question - DOPE,
Charlie Allerston
- [modeller_usage] loop modeling,
Mehdi Bagheri-Hamaneh
- [modeller_usage] Question,
Manuel Aguilar
- [modeller_usage] I am having problems to install the MODELLER,
gpereira
- [modeller_usage] Disulfides,
Joel Tyndall
- Re: [modeller_usage] D-Proline problem,
N.Arun Prasanna
- [modeller_usage] using different weights for spatial restraints,
Lillian Chong
- [modeller_usage] modeling a 2 domain protein with interdomain restraints,
Michel Seigneuret
- [modeller_usage] Making bond between residue and BLK residue,
서주현
- [modeller_usage] complete_pdb,
Tamas Hegedus
- [modeller_usage] orientation of domains in chimera,
Lillian chong
- [modeller_usage] clustering,
Miriam Leach
- [modeller_usage] Specify Angle Restraint,
Brandon Mills
- [modeller_usage] RMSD,
Mathew Smith
- [modeller_usage] arranging individual subunits,
adak nasiripour
- [modeller_usage] modelling of sequence without structural template.,
Archana Chavan
- [modeller_usage] help with modelling protein-DNA complex,
Elliott Stollar
- [modeller_usage] modelling a protein-receptor complex,
Eva Vanamee
- [modeller_usage] Creating a dimer using model generated by modeller,
Charlie Allerston
- [modeller_usage] changes in MODELLER9 optimization & DNA denaturation,
RYAN PAVLOVICZ
- [modeller_usage] Errors during generate alignment file for two chains,
jitrayut jitonnom
- [modeller_usage] secondary structure assignment and patching,
Ryan
- [modeller_usage] query,
deepti
- [modeller_usage] How can modeller build the structure of antibodies ?,
jitrayut jitonnom
- Re: [modeller_usage] How can modeller build the structure of antibodies ?,
jitrayut jitonnom
- [modeller_usage] How to incorporate NAD and water in my model,
deepti
- [modeller_usage] how to select the best template?,
deepti
- [modeller_usage] HYP and alignment from other than modeller,
yuemin liu
- [modeller_usage] alignment of multiple templates,
Bo Yang
- [modeller_usage] [Fwd: modeling crosslinked homodimeric protein],
Modeller Caretaker
- [modeller_usage] Quesion about patch the Terminal residues,
zhou jinming
- [modeller_usage] Targeting Restraints for Weakening,
Brandon Mills
- [modeller_usage] [Fwd: molecular dynamics simulations in modeller],
Modeller Caretaker
- [modeller_usage] model ligand,
Bo Yang
- [modeller_usage] Modeling multiple chains with two ligands,
Dimitry.A.Suplatov
- Re: [modeller_usage] modeller_usage Digest, Vol 6, Issue 29,
Dimitry.A.Suplatov
- [modeller_usage] User defined restraints,
Dimitry.A.Suplatov
- [modeller_usage] Rigid ligand,
dimitry.a.suplatov
- [modeller_usage] Add rigid bodies and CA-CA restraints,
Gregoire Depret
- [modeller_usage] Psi and Phi Dihedral Restraints,
Brandon Mills
- [modeller_usage] using model-loop-refine in Modeller9v1,
- Re: [modeller_usage] using model-loop-refine in Modeller9v1,
- [modeller_usage] using model-addrsr in modeller9v1,
- [modeller_usage] Rigid bodies on the backbone only.,
Gregoire Depret
- [modeller_usage] stuck even before begining - how to create the .ali file,
Ariel Bensimon
- [modeller_usage] using multiple template in Modeller9v1,
- [modeller_usage] Unpick restraints and partial optimization.,
Gregoire Depret
- [modeller_usage] CONECT record in MODELLER?,
Ngo Duc Tri
- [modeller_usage] Ubuntu installation issue,
Christian Meesters
[modeller_usage] [Fwd: Cannot generate the plot of DOPE?],
Modeller Caretaker
[modeller_usage] getting pdb's but not fit.pdb's,
roac0030
[modeller_usage] Modeller as webservice (WSDL),
Francoijs, Kees-Jan
[modeller_usage] query about chimeric protein,
Sana Bilal
[modeller_usage] problems modeling a multimer,
Douglas Kojetin
[modeller_usage] loop to connect two domain,
Jayapal, Prabha
[modeller_usage] Optimizing the Helix strain in the model?,
Ngo Duc Tri
[modeller_usage] Making many result model,
서주현
[modeller_usage] use bovin rhodopsin as template,
[modeller_usage] model transmenbrane regions,
[modeller_usage] disulfide,
Lixia Jin
[modeller_usage] Including disulfide bonds,
Atila Iamarino
[modeller_usage] ImportError: No module named automodel...,
matteo
[modeller_usage] define residues,
Lixia Jin
[modeller_usage] residue selection,
Lixia Jin
[modeller_usage] to build a structure from CA coordinate,
Lixia Jin
[modeller_usage] difficult modelling example,
James Fethiere
[modeller_usage] Model with ligand from template,
hori koshii
[modeller_usage] a question about add hidrogen,
Atila Iamarino
[modeller_usage] help--model-segment.py,
[modeller_usage] model-multiple.py error,
Eeson Rajendra
[modeller_usage] modweb,
James Fethiere
[modeller_usage] h-bonds with loop models,
David Gell
[modeller_usage] build_profile.py help,
Eeson Rajendra
[modeller_usage] model.energy(),
Jayapal, Prabha
[modeller_usage] homology problem,
Fabian Glaser
[modeller_usage] How to bend a helix?,
"Nadine Töpfer"
[modeller_usage] what should PYTHONPATH and LD_LIBRARY_PATH be set to?,
David Mobley
[modeller_usage] modelling a chimera from structureM-type templates,
Cahya Prihatna
[modeller_usage] set alpha-helix and SS bond,
Aline
[modeller_usage] Loop Modelling,
Michael Paterson
[modeller_usage] Alignment problem,
Monika Sharma
[modeller_usage] Sequence alignment softwares,
DPF Chocolate
[modeller_usage] setting restyp, top_heav and par libs,
David Marshall
[modeller_usage] Help with transfer_xyz method,
Ali Algarrous
[modeller_usage] ternary complex in modweb,
James Fethiere
[modeller_usage] Same values for the models,
Atila Iamarino
[modeller_usage] same values for the models 2,
Atila Iamarino
[modeller_usage] pdb95.fsa,
Bo Yang
[modeller_usage] How to optimize a model,
Atila Iamarino
[modeller_usage] modeller 9.2: spaghetti effect with multiple templates,
Raik Gruenberg
[modeller_usage] disulphide,
Thijs Beuming
[modeller_usage] DOPE score question,
hori koshii
[modeller_usage] trouble modeling ligand,
Starr Hazard
[modeller_usage] Block Ligand stereo chemistry problem,
Andre Fischer
[modeller_usage] making a patch work,
Starr Hazard
[modeller_usage] Question about a protein structure,
Ester Fusté Domínguez
[modeller_usage] regarding simulated annealing,
vidhya sankar
[modeller_usage] [Fwd: five ss bridges],
Modeller Caretaker
[modeller_usage] The models miss the 40 first aa of the sequence,
Dany Naranjo Feliciano
[modeller_usage] five ss bridges,
Dany Naranjo Feliciano
[modeller_usage] [Fwd: Re: The models miss the 40 first aa of the sequence],
Modeller Caretaker
[modeller_usage] Could you please remove my e-mail from your list? Thank you,
Omid Khalouei
[modeller_usage] total of DOPE per residues not equal to global DOPE?,
hori koshii
[modeller_usage] automated response,
charloteaux.b
[modeller_usage] modelling tetramer by using multiple templates,
EP
[modeller_usage] Global DOPE vs. local profile,
hori koshii
Re: [modeller_usage] loop refinement,
Agnieszka Szarecka
Re: [modeller_usage] loop refinement,
Modeller Caretaker
<Possible follow-ups>
[modeller_usage] Loop refinement,
ESTER FUSTE DOMINGUEZ
[modeller_usage] loop refinement,
Laura Lopez
[modeller_usage] Modeller 9v2 release,
Modeller Caretaker
[modeller_usage] Error Messages,
Michael Paterson
[modeller_usage] code and logic question,
Christian Meesters
[modeller_usage] DOPE,
Ester Fusté Domínguez
[modeller_usage] regarding DOPE score,
vidhya sankar
[modeller_usage] regrding superpose.py,
vidhya sankar
[modeller_usage] ref: SUPERPOSE.PY,
vidhya sankar
Re: [modeller_usage] SA IN optimize.py,
vidhya sankar
Re: [modeller_usage] log files,
vidhya sankar
Re: [modeller_usage] dope calculations,
vidhya sankar
Re: [modeller_usage] superpose.py,
vidhya sankar
[modeller_usage] Reg. Generating profile plot using GNUPLOt,
saravanan
[modeller_usage] restraints from multiple templates,
Mathew Smith
[modeller_usage] loop optimization in the presence of a ligand,
Thijs Beuming
Re: [modeller_usage] modeller_usage Digest, Vol 6, Issue 79,
vidhya sankar
Re: [modeller_usage] warning rectifications,
vidhya sankar
[modeller_usage] Regarding violations profile,
harpreet singh
[modeller_usage] help--orient multiple template,
[modeller_usage] align sequences,
rgerber2
Re: [modeller_usage] Secondary Structure Restraints,
Modeller Caretaker
[modeller_usage] help--model_ini.py,
[modeller_usage] Reg. comparing dope profile or both template and model,
saravanan
Re: [modeller_usage] Reg. comparing dope profile or both template and model,
saravanan
[modeller_usage] applying symmetry,
Christian Meesters
[modeller_usage] Reg. align_codes error in profile_build.py in Mod9v2,
saravanan
[modeller_usage] ligand modeling in binding site,
mahendra awale
[modeller_usage] ligand modeling in binding site of protein,
mahendra awale
[modeller_usage] Modeling a sequence based on a low identity to a template,
ESTER FUSTE DOMINGUEZ
[modeller_usage] ERROR MESSAGE,
ESTER FUSTE DOMINGUEZ
[modeller_usage] Problem when reconstruct the protein with know structure!,
liu xin
[modeller_usage] multiple-template no overlap,
[modeller_usage] platform (in)dependent libraries?,
Mike White
[modeller_usage] structural docking,
rgerber2
[modeller_usage] setting distance restraints,
Mike White
[modeller_usage] Modelling complexes,
saccenti
[modeller_usage] modeller.top location?,
DANIEL TAYLOR
[modeller_usage] Model quality assessment,
saccenti
[modeller_usage] Special Considerations in Membrane-bound models?,
Andrew D. Fant
[modeller_usage] align_codes error,
Dave Roe
[modeller_usage] dope_loopmodel question,
Mike White
[modeller_usage] Cu(I) Parameters,
saccenti
[modeller_usage] using DOPE assessment,
saccenti
[modeller_usage] selection to model,
Alex Brown
[modeller_usage] model_comparison,
Prasenjit Mukherjee
Re: [modeller_usage] September 70% OFF,
Viagra.com Inc
[modeller_usage] help,
huifang liu
[modeller_usage] disulfide bonds in aligned structures?,
Mike White
[modeller_usage] regarding loop refinement,
simran jeet
[modeller_usage] Mutations,
laura . buttazzo
[modeller_usage] _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 1CPG,
DANIEL TAYLOR
[modeller_usage] Models from secondary structure and distance constraints alone?,
Andrew D. Fant
[modeller_usage] Modeling of a C-terminal segment,
Bo Yang
[modeller_usage] entangled domains,
Russell Green
[modeller_usage] qsub and cis restraints,
Gordon Wells
[modeller_usage] exploding GTP,
Jonathan Winger
[modeller_usage] Class mymodel: How to randomize coordinates,
Baptiste Legrand
Re: [modeller_usage] RE : Re: Class mymodel: How to randomize coordinates,
Modeller Caretaker
[modeller_usage] Warning messages,
csreddy
[modeller_usage] regarding N terminus region,
simran jeet
[modeller_usage] ImportError: No module named socket (or math),
Greipel . Joachim
[modeller_usage] Reg. model_energies.py,
Saravanan
[modeller_usage] RMSD based clustering of models,
csreddy
[modeller_usage] how to generate large number of models without using automodel class,
harpreet singh
[modeller_usage] Refine,
Dany Naranjo Feliciano
[modeller_usage] plotdope problem,
jacques deruchoud
[modeller_usage] validation,
Adriana Esteves
[modeller_usage] validation with procheck,
Adriana Esteves
[modeller_usage] Asking about energy minimization after initial model,
Chiranjit Chowdhury
[modeller_usage] query about alignment type,
Bhavya Jindal
[modeller_usage] DOPE applied to multichains,
DimitryASuplatov
[modeller_usage] Transfer_xyz question,
Ali Algarrous
[modeller_usage] symmetry in automodel,
Gordon Wells
[modeller_usage] Asking about energy minimization after initial model],
Chiranjit Chowdhury
[modeller_usage] Fwd: validation and log file,
aesteves
[modeller_usage] ligand,
aesteves
[modeller_usage] ligand 2,
aesteves
[modeller_usage] Writing out chain ID in the PDB,
Vadim Patsalo
[modeller_usage] Modeller creating strange structures,
Russell Green
[modeller_usage] HOH,
Adriana Esteves
[modeller_usage] November 72% OFF,
Canadian Doctor Willa Gillespie
[modeller_usage] alignment_question,
Urszula Uciechowska
[modeller_usage] comparing models,
simonagi
[modeller_usage] PIR format,
Urszula Uciechowska
[modeller_usage] Alignment editors?,
Esben Jannik Bjerrum
[modeller_usage] mutate model,
suji george
[modeller_usage] post translational modification,
suji george
[modeller_usage] Modeller,
Nataly Amorim
[modeller_usage] Modelling long alpha-chains,
DimitryASuplatov
[modeller_usage] Dope output?,
Dany Naranjo Feliciano
[modeller_usage] model-loop,
Urszula Uciechowska
[modeller_usage] multiple target sequences,
Han Choe
Re: [modeller_usage] December 74% OFF,
Doctor Harriett Lacey
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