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searching for PyMOL 75 found (138 total)

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Α-Mannosidase (324 words) [view diff] case mismatch in snippet view article find links to article

used in vaccine development. A deficiency can lead to α-mannosidosis. "PyMol". Schrodinger. Retrieved 2011-09-14. Suits, MDL; Yanping Zhu; Edward J.

Nucleic acid tertiary structure (6,380 words) [view diff] exact match in snippet view article find links to article

doi:10.1126/science.1153803. PMC 4406475. PMID 18388288.; rendered with PyMOL PDB: 2K95; Kim NK, Zhang Q, Zhou J, Theimer CA, Peterson RD, Feigon J (December

Ribose-phosphate diphosphokinase (1,500 words) [view diff] case mismatch in snippet view article find links to article

PyMol rendering of one subunit of the enzyme phosphoribosyl pyrophosphate synthetase I (human). Flexible loop colored in green; ribose 5-phosphate binding

Cholesterol 24-hydroxylase (2,008 words) [view diff] exact match in snippet view article find links to article

cholesterol 3-sulfate. Hydrophobic residues interacting with the aliphatic tail of the cholesterol are labelled in white. Created in pyMOL from PDB 2Q9F

AT-hook (833 words) [view diff] case mismatch in snippet view article find links to article

focus on the central region of the AT-hook. Shown in magenta are the side chains Pro35, Arg36, Gly37, Arg38, and Pro39. Made with PyMol. PDB code: 3UXW.

Acetyl-CoA synthetase (2,150 words) [view diff] exact match in snippet view article find links to article

Biochemistry. 42 (10): 2866–73. doi:10.1021/bi0271603. PMID 12627952. The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. Mews P, Donahue

Glucocerebrosidase (2,001 words) [view diff] case mismatch in snippet view article find links to article

(I-III). Three-dimensional PyMol rendering of glucocerebrosidase with three domains highlighted. Three-dimensional PyMol rendering of glucocerebrosidase

Propionyl-CoA carboxylase (1,718 words) [view diff] exact match in snippet view article find links to article

fit the cryo-EM map. All the structure figures were produced with PyMOL (www.pymol.org), and the cryo-EM figures were produced with Chimera. This provides

Schrödinger, Inc. (577 words) [view diff] exact match in snippet view article find links to article

computational platform for drug discovery and materials science LiveDesign PyMOL Revenue $181 Million (2022) Number of employees 1015 Website www.schrodinger

PROB1 (903 words) [view diff] exact match in snippet view article find links to article

structure prediction for PROB1 was generated using I-Tasser and rendered in PyMOL; overall, the protein displays an elongated structure. Analysis of protein

Cellulose 1,4-β-cellobiosidase (non-reducing end) (833 words) [view diff] case mismatch in snippet view article

CBH1 Structure, generated using pymol

Pyruvate dehydrogenase complex (3,219 words) [view diff] case mismatch in snippet view article find links to article

Pymol-generated image of E1 subunit of pyruvate dehydrogenase complex in E. Coli

TRNA-intron endonuclease (2,613 words) [view diff] case mismatch in snippet view article find links to article

Pymol image of the α4 structure in Methanocaldococcus jannaschii (PBD: 1A79).

Curcumin synthase (1,624 words) [view diff] exact match in snippet view article find links to article

specificity of curcumin synthase for the CoA moiety. The triad, displayed in a PyMOL image below, despite being buried in each monomer, is connected to the surface

Halovir (1,968 words) [view diff] case mismatch in snippet view article find links to article

1007/978-1-4684-8580-6_9, ISBN 978-1-4684-8580-6, retrieved 2022-10-10 "Support | pymol.org". pymol.org. Retrieved 2022-11-27. Jen, W. -C.; Jones, G. A.; Brewer, D.;

Β-Glucosidase (1,303 words) [view diff] exact match in snippet view article find links to article

(1): 46–56. doi:10.1016/j.jsb.2010.07.008. PMID 20682343.; rendered via PyMOL. Cox M, Lehninger AL, Nelson DR (2000). Lehninger principles of biochemistry

Ca2+/calmodulin-dependent protein kinase II (3,458 words) [view diff] case mismatch in snippet view article find links to article

The structure of the association domain of CaMKII gamma rendered by pymol from PDB 2ux0 (left) space fill holoenzyme (center) cartoon holoemzyme (right)

Orotidine 5'-phosphate decarboxylase (1,182 words) [view diff] case mismatch in snippet view article find links to article

BMP. Note the Lys and Asp residues surrounding the 6-hydroxyl of the substrate. (Image captured from pymol viewer snapshot of 1LOR crystal structure)

CD32 (1,163 words) [view diff] exact match in snippet view article find links to article

doi:10.1093/emboj/18.5.1095. PMC 1171201. PMID 10064577.; rendered via PyMOL. Lisi S, Sisto M, Lofrumento DD, D'Amore S, D'Amore M (March 2011). "Advances

Pyruvate dehydrogenase (1,279 words) [view diff] case mismatch in snippet view article find links to article

dehydrogenase E1 subunit of E. coli. Colors represent different chains. Structure determined by Arjunan et al. Biochemistry 2002. Created with PyMol.

APOBEC (751 words) [view diff] exact match in snippet view article find links to article

doi:10.1038/nature05492. PMID 17187054. S2CID 4394772.; rendered using PyMOL. Wedekind JE, Dance GS, Sowden MP, Smith HC (April 2003). "Messenger RNA

Prokaryotic large ribosomal subunit (1,476 words) [view diff] case mismatch in snippet view article find links to article

subunit. Proteins are colored in blue and RNA in ochre. The active site, adenine 2486, is highlighted in red. Image created from PDB: 3CC2 using PyMol

S100 protein (1,164 words) [view diff] exact match in snippet view article find links to article

S100/ICaBP type calcium binding domain Structure of the S100B protein. Based on PyMOL rendering of PDB 1b4c. Identifiers Symbol S_100 Pfam PF01023 InterPro IPR013787

Caspase 3 (3,392 words) [view diff] case mismatch in snippet view article find links to article

and p17 (light blue) subunits of caspase-3 with the beta-sheet structures of each in red and blue, respectively; image generated in Pymol from 1rhm.pdb

Complex lasso proteins (1,085 words) [view diff] case mismatch in snippet view article find links to article

The manual inspection of the data is also possible with the PyLasso - the PyMol plugin. Knotted proteins Li, Yanyan; Zirah, Séverine; Rebuffat, Sylvie (2015)

Phosphoenolpyruvate carboxylase (1,883 words) [view diff] exact match in snippet view article find links to article

Phosphoenolpyruvate (PEP) carboxylase single subunit structure (generated by PyMOL)] Identifiers EC no. 4.1.1.31 CAS no. 9067-77-0 Databases IntEnz IntEnz

Transfer-messenger RNA (3,310 words) [view diff] case mismatch in snippet view article find links to article

domain consists of the 3' and 5' ends of the tmRNA. Image was created using Pymol molecular imaging software and data obtained from the RCSB Protein Data

OmpT (1,367 words) [view diff] exact match in snippet view article find links to article

Protease 7 Crystal Structure of OmpT visualised in PyMOL, lateral and aerial views (PDB: 1I78). Identifiers Organism Escherichia coli (strain K12) Symbol

Ornithine decarboxylase (2,082 words) [view diff] exact match in snippet view article find links to article

295 (1): 7–16. doi:10.1006/jmbi.1999.3331. PMID 10623504.; rendered via PyMOL. Pendeville H, Carpino N, Marine JC, Takahashi Y, Muller M, Martial JA,

Serine hydroxymethyltransferase (2,378 words) [view diff] case mismatch in snippet view article find links to article

PyMol rendered crystal structure of serine hydroxymethyltransferase

Platelet-derived growth factor receptor (1,563 words) [view diff] exact match in snippet view article find links to article

doi:10.1073/pnas.1000806107. PMC 2895058. PMID 20534510.; rendered using PyMOL. Williams LT (March 1989). "Signal transduction by the platelet-derived

History of molecular biology (7,533 words) [view diff] exact match in snippet view article find links to article

doi:10.1126/science.1153803. PMC 4406475. PMID 18388288.; rendered with PyMOL PDB: 1FFK; Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (August 2000)

FAN1 (1,817 words) [view diff] exact match in snippet view article find links to article

blue and purple, TPR in orange, and VRR_Nuc in green. The secondary features of the SAP domain are labeled. Created in PyMOL from PDB structure 4RID.

Mannose 6-phosphate receptor (2,963 words) [view diff] case mismatch in snippet view article find links to article

(Domains 1, 2 and 3) of the cation-independent mannose 6-phosphate receptor with its ligand bound. Image generated from PDB file: = 1SZ0 1SZ0 using PyMol.

UTP—glucose-1-phosphate uridylyltransferase (2,932 words) [view diff] case mismatch in snippet view article find links to article

uridylyltransferase Human UTP—glucose-1-phosphate uridylyltransferase cartoon created in pymol Identifiers EC no. 2.7.7.9 CAS no. 9026-22-6 Databases IntEnz IntEnz view

ProtCID (717 words) [view diff] case mismatch in snippet view article find links to article

activation. Each monomer is colored from blue to red from N to C terminus. ProtCID provides PyMol scripts for each cluster to produce similar images.

6-Pyruvoyltetrahydropterin synthase (996 words) [view diff] case mismatch in snippet view article find links to article

6-Pyruvoyltetrahydropterin synthase PTPS enzyme pymol pretty Identifiers EC no. 4.2.3.12 CAS no. 97089-82-2 Databases IntEnz IntEnz view BRENDA BRENDA

Sucrose synthase (553 words) [view diff] exact match in snippet view article find links to article

doi:10.1074/jbc.M111.275974. PMC 3195635. PMID 21865170.; rendered with PyMOL Avigad G; Milner Y (1966). "UDP-glucose: Fructose transglucosylase from

Acyl-CoA dehydrogenase (NADP+) (279 words) [view diff] exact match in snippet view article

Worldwide Protein Data Bank. doi:10.2210/pdb3hzz/pdb.; rendered using PyMOL. Dommes V, Luster W, Cvetanovic M, Kunau WH (1982). "Purification by affinity

XPO5 (1,304 words) [view diff] case mismatch in snippet view article find links to article

Image of XPO5 ternary complex generated in PyMol from crystal structure entry 3A6P in the Protein Data Bank. XPO5 is labeled green, Ran is labeled red

Methyl-accepting chemotaxis proteins (884 words) [view diff] exact match in snippet view article find links to article

(2): 186–201. doi:10.1006/jmbi.1996.0507. PMID 8831788.; rendered with PyMOL Kim SH, Prive GG, Pandit J, Koshland DE, Yeh JI, Biemann HP (1996). "High-resolution

Ribonuclease 4 (929 words) [view diff] case mismatch in snippet view article find links to article

Shown is a PyMol image of the ribonuclease 4 dimer, blue, with deoxyuridine monophosphate , white, in the active site. PDB: 2RNF

Angiotensin-converting enzyme (2,536 words) [view diff] exact match in snippet view article find links to article

lisinopril, zinc cation shown in grey, chloride anions in yellow. Based on PyMOL rendering of PDB 1o86. The picture shows that lisinopril is a competitive

Ascorbate peroxidase (1,255 words) [view diff] case mismatch in snippet view article find links to article

the heme group (also in red). Image taken from PDB 1OAF and created using Pymol Identifiers EC no. 1.11.1.11 CAS no. 72906-87-7 Databases IntEnz IntEnz

METAP2 (3,068 words) [view diff] case mismatch in snippet view article find links to article

Figure 1. Active site structure of MetAP2. Generated using PDB:1BOA in PyMol. Click to view rotatable structure

Plasminogen activator inhibitor-2 (2,905 words) [view diff] case mismatch in snippet view article find links to article

Reactive center loop (RCL) of plasminogen activator inhibitor-2. PyMol rendering of PDB 2ARR.

Chorismate synthase (1,115 words) [view diff] exact match in snippet view article find links to article

(2): 130–143. doi:10.1016/j.jsb.2005.12.008. PMID 16459102.; rendered with PyMOL Schaller A, Schmid J, Leibinger U, Amrhein N (1991). "Molecular cloning

Cellulase (2,978 words) [view diff] exact match in snippet view article find links to article

36 (51): 16032–9. doi:10.1021/bi972407v. PMID 9440876.; rendered with PyMOL Barkalow DG, Whistler RL. "Cellulose". AccessScience, McGraw-Hill.[permanent

MMP3 (3,031 words) [view diff] exact match in snippet view article find links to article

catalytic zinc (purple). Calcium ions (yellow) are also shown. Based on the PyMOL rendering of PDB 1UEA. For simplicity, the other MMP-3 monomer complexed

GDP-mannose 4,6-dehydratase (974 words) [view diff] case mismatch in snippet view article find links to article

Here is a pymol view of the entire structure of the GDP-Mannose 4, 6-Dehydratase enzyme.

Marnaviridae (4,499 words) [view diff] exact match in snippet view article find links to article

the structural analysis of the capsid's cryo-EM maps and atomic models, PyMOL 1.4 was used to obtain a Root-Mean-Square-Deviated (RMSD) per residue, which

Dimethylargininase (1,125 words) [view diff] exact match in snippet view article find links to article

8624–8635. doi:10.1021/bi9007098. PMC 2746464. PMID 19663506.; rendered via PyMOL. Leiper JM, Santa Maria J, Chubb A et al. Identification of two human dimethylarginine

Epoxide hydrolase (2,208 words) [view diff] exact match in snippet view article find links to article

doi:10.1016/j.jmb.2008.06.030. PMC 2866126. PMID 18585390.; rendered via PyMOL Morisseau C (January 2013). "Role of epoxide hydrolases in lipid metabolism"

Zingibain (1,872 words) [view diff] case mismatch in snippet view article find links to article

Zingibain PYMOL generated 3D structure of zingibain monomer Identifiers EC no. 3.4.22.67 CAS no. 246044-91-7 Databases IntEnz IntEnz view BRENDA BRENDA

PreQ1 riboswitch (2,055 words) [view diff] exact match in snippet view article find links to article

PreQ1 structures Left: Free structure (PDB: 3Q51) Right: Bound structure(PDB: 3Q50) . Both generated by PyMOL using existing crystal structures .

Direct coupling analysis (3,331 words) [view diff] exact match in snippet view article find links to article

Archived 2017-01-15 at the Wayback Machine Useful applications: DCA-MOL: a PyMOL plugin to analyze DCA results on a structure Morcos, F.; Pagnani, A.; Lunt

Azurin (1,658 words) [view diff] case mismatch in snippet view article find links to article

The copper binding domain of azurin rendered in PyMol, with four of the five copper-binding ligands labeled. The distance (in angstroms) from the copper

Fibroblast growth factor receptor 1 (5,001 words) [view diff] case mismatch in snippet view article find links to article

activation segment. The figure is generated through Molprobity extension on Pymol. Figure 2. Hydrogen bonds at pY766 Figure 3. Closed conformation in Inactive

Electron localization function (910 words) [view diff] exact match in snippet view article find links to article

Image of the ELF of water at level 0.8, generated using PyMOL

DNA damage-inducible transcript 3 (5,505 words) [view diff] exact match in snippet view article find links to article

CHOP protein structure created with PyMOL

De novo protein structure prediction (2,572 words) [view diff] exact match in snippet view article find links to article

[UniParc]) Tertiary structure of human artemin (PDB: 2GYR) rendered using PyMOL (Delano Scientific Freeware) De novo conformation predictors usually function

Glyoxylate reductase (1,322 words) [view diff] exact match in snippet view article find links to article

hyperthermophilic archaeon, Pyrococcus horikoshii OT3. Image created by PyMOL. Identifiers EC no. 1.1.1.26 CAS no. 9028-32-4 Databases IntEnz IntEnz view

Photoactive yellow protein (1,148 words) [view diff] exact match in snippet view article find links to article

the innate oxyanion hole. To the left is a crystallographic image of p-coumaric acid in the ligand binding site based on PDB: 2PYP PyMOL rendering.

Geosmin synthase (1,511 words) [view diff] exact match in snippet view article find links to article

(4): 725–38. doi:10.1038/nprot.2010.5. PMC 2849174. PMID 20360767. The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC. Q9X839 (CYC2_STRCO)

12-oxophytodienoate reductase (1,420 words) [view diff] case mismatch in snippet view article find links to article

Structure of 12-oxophytodienoate reductase (OPR3) bound to FMN cofactor, created in Pymol.

CXorf38 Isoform 1 (2,567 words) [view diff] case mismatch in snippet view article find links to article

Ribbon structure of CXorf38, predicted by I-TASSER and annotated in Pymol.

Zero ionic layer (1,319 words) [view diff] case mismatch in snippet view article find links to article

SNARE complex zoomed in to the zero ionic layer level on Pymol simulator

SMCO3 (1,203 words) [view diff] case mismatch in snippet view article find links to article

Predicted structure of SMCO3 created using iTasser and PYMOL.

Undecaprenyl phosphate N,N'-diacetylbacillosamine 1-phosphate transferase (1,920 words) [view diff] case mismatch in snippet view article find links to article

Structure of the protein PglC from Campylobacter concisus. Based on PyMol rendering of PDB 5W7L.

Cyanase (1,543 words) [view diff] case mismatch in snippet view article find links to article

residues are arginines and provide a catalytic pocket for the enzyme mechanism to take place. Created in PyMol from http://www.rcsb.org/structure/6B6M.

GlycoRNA (1,400 words) [view diff] case mismatch in snippet view article find links to article

PYMOL: Three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum. (PDB: 1PGS)

SBGrid Consortium (790 words) [view diff] exact match in snippet view article find links to article

including Geneious for cloning and bioinformatics, incentive builds for PyMOL, and for North American labs, the Schrödinger Small-Molecule Drug Discovery

DNA-3-methyladenine glycosylase (2,589 words) [view diff] case mismatch in snippet view article find links to article

Human Alkyladenine DNA Glycosylase's structure generated with Pymol

Leadzyme (1,847 words) [view diff] case mismatch in snippet view article find links to article

leadzyme. The green spheres represent Mg2+ ions and the red spheres represent Sr2+ ions.Figure rendered in pymol using coordinates from pdb file 1NUV.

List of sequence alignment software (2,355 words) [view diff] exact match in snippet view article find links to article

function sampling via dynamic programming Both Global U. Mückstein 2002 PyMOL "align" command aligns sequence & applies it to structure Protein Global