المؤلفون: Honorato RV; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Trellet ME; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Fluigent, Le Kremlin-Bicêtre, France., Jiménez-García B; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Zymvol Biomodeling SL, Barcelona, Spain., Schaarschmidt JJ; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Eggenstein-Leopoldshafen, Germany., Giulini M; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Reys V; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Koukos PI; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Biomedical Research Foundation, Academy of Athens, Athens, Greece., Rodrigues JPGLM; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Schrödinger Inc., New York, NY, USA., Karaca E; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Izmir Biomedicine and Genome Center, Izimir, Turkey., van Zundert GCP; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Schrödinger Inc., New York, NY, USA., Roel-Touris J; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Protein Design and Modeling Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain., van Noort CW; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jandová Z; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Boehringer Ingelheim International GmbH, Vienna, Austria., Melquiond ASJ; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.; Utrecht Medical Center, Utrecht, the Netherlands., Bonvin AMJJ; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl.

المصدر: Nature protocols [Nat Protoc] 2024 Jun 17. Date of Electronic Publication: 2024 Jun 17.

نوع المنشور: Journal Article; Review

بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101284307 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1750-2799 (Electronic) Linking ISSN: 17502799 NLM ISO Abbreviation: Nat Protoc Subsets: MEDLINE

المؤلفون: Allahyar A; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Pieterse M; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Swennenhuis J; Cergentis BV, Utrecht, the Netherlands., Los-de Vries GT; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Yilmaz M; Cergentis BV, Utrecht, the Netherlands., Leguit R; University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands., Meijers RWJ; University Medical Centre Utrecht, Department of Pathology, Utrecht, the Netherlands., van der Geize R; Laboratorium Pathologie Oost-Nederland, Hengelo, the Netherlands., Vermaat J; Leiden University Medical Centre, Department of Hematology, Leiden, the Netherlands., Cleven A; Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands., van Wezel T; Leiden University Medical Center, Department of Pathology, Leiden, the Netherlands., Diepstra A; University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands., van Kempen LC; University of Groningen, University Medical Centre Groningen, Department of Pathology & Medical Biology, Groningen, the Netherlands., Hijmering NJ; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Stathi P; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Sharma M; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Melquiond ASJ; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., de Vree PJP; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Verstegen MJAM; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Krijger PHL; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Hajo K; Cergentis BV, Utrecht, the Netherlands., Simonis M; Cergentis BV, Utrecht, the Netherlands., Rakszewska A; Cergentis BV, Utrecht, the Netherlands., van Min M; Cergentis BV, Utrecht, the Netherlands., de Jong D; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Ylstra B; Amsterdam UMC-Vrije Universiteit Amsterdam, Department of Pathology and Cancer Center Amsterdam, Amsterdam, the Netherlands., Feitsma H; Cergentis BV, Utrecht, the Netherlands., Splinter E; Cergentis BV, Utrecht, the Netherlands. erik.splinter@cergentis.com., de Laat W; Oncode Institute & Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. w.laat@hubrecht.eu.

المصدر: Nature communications [Nat Commun] 2021 Jun 07; Vol. 12 (1), pp. 3361. Date of Electronic Publication: 2021 Jun 07.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

مواضيع طبية MeSH: Translocation, Genetic*, High-Throughput Nucleotide Sequencing/*methods , Lymphoma, B-Cell/*genetics , Lymphoma, Non-Hodgkin/*genetics , Paraffin Embedding/*methods , Tissue Fixation/*methods, Computational Biology/methods ; Gene Rearrangement ; Genes, bcl-2/genetics ; Genes, myc/genetics ; Humans ; In Situ Hybridization, Fluorescence/methods ; Lymphoma, B-Cell/diagnosis ; Lymphoma, Non-Hodgkin/diagnosis ; Proto-Oncogene Proteins c-bcl-6/genetics ; Reproducibility of Results ; Retrospective Studies ; Sensitivity and Specificity

المؤلفون: Koukos PI; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Roel-Touris J; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Ambrosetti F; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.; Department of Physics, Sapienza University, Rome, Italy., Geng C; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Schaarschmidt J; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.; Multiscale Materials Modelling and Virtual Design, Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany., Trellet ME; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Melquiond ASJ; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Xue LC; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Honorato RV; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Moreira I; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.; CNC-Center for Neuroscience and Cell Biology, Rua Larga, FMUC, Polo I, 1° andar, Universidade de Coimbra, Coimbra, Portugal., Kurkcuoglu Z; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Vangone A; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands., Bonvin AMJJ; Faculty of Science, Department of Chemistry, Bijvoet Center for Biomolecular Research, Computational Structural Biology Group, Utrecht University, Utrecht, The Netherlands.

المصدر: Proteins [Proteins] 2020 Aug; Vol. 88 (8), pp. 1029-1036. Date of Electronic Publication: 2020 Jan 07.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

مواضيع طبية MeSH: Molecular Docking Simulation* , Software*, Peptides/*chemistry , Proteins/*chemistry, Amino Acid Sequence ; Binding Sites ; Humans ; Ligands ; Peptides/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Multimerization ; Proteins/metabolism ; Research Design ; Structural Homology, Protein ; Thermodynamics

المؤلفون: Lensink MF; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Brysbaert G; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Nadzirin N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Chaleil RAG; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Gerguri T; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Bates PA; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Laine E; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France., Carbone A; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.; Institut Universitaire de France (IUF), Paris, France., Grudinin S; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Kong R; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Liu RR; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Xu XM; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Shi H; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Chang S; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Eisenstein M; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel., Karczynska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Lubecka E; Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland., Lipska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Krupa P; Polish Academy of Sciences, Institute of Physics, Warsaw, Poland., Mozolewska M; Polish Academy of Sciences, Institute of Computer Science, Warsaw, Poland., Golon Ł; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Samsonov S; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea., Crivelli S; Department of Computer Science, UC Davis, Davis, California., Pagès G; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Karasikov M; Department of Computer Science, ETH, Zurich, Switzerland., Kadukova M; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia., Yan Y; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Huang SY; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Rosell M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Rodríguez-Lumbreras LA; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Romero-Durana M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Díaz-Bueno L; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Fernandez-Recio J; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain.; Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain., Christoffer C; Department of Computer Science, Purdue University, West Lafayette, Indiana., Terashi G; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Shin WH; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Aderinwale T; Department of Computer Science, Purdue University, West Lafayette, Indiana., Maddhuri Venkata Subraman SR; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kihara D; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kozakov D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Vajda S; Department of Biomedical Engineering, Boston University, Boston, Massachusetts.; Department of Chemistry, Boston University, Boston, Massachusetts., Porter K; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Padhorny D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Desta I; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Beglov D; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Ignatov M; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Kotelnikov S; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Moal IH; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Ritchie DW; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Chauvot de Beauchêne I; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Maigret B; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Devignes MD; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Ruiz Echartea ME; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Barradas-Bautista D; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cao Z; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cavallo L; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Oliva R; Department of Sciences and Technologies, University of Naples 'Parthenope', Napoli, Italy., Cao Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Baek M; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Park T; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Woo H; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Seok C; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Braitbard M; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel., Bitton L; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Scheidman-Duhovny D; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Dapkūnas J; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Olechnovič K; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Venclovas Č; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Kundrotas PJ; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Belkin S; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Chakravarty D; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Badal VD; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vakser IA; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vreven T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Vangaveti S; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Borrman T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Weng Z; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Guest JD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Xu X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Duan R; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Qiu L; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Hou J; Department of Computer Science, University of Missouri, Columbia, Missouri., Ryan Merideth B; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Ma Z; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri., Cheng J; Department of Computer Science, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Zou X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.; Department of Biochemistry, University of Missouri, Columbia, Missouri., Koukos PI; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Roel-Touris J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Ambrosetti F; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Geng C; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Schaarschmidt J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Trellet ME; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Melquiond ASJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Xue L; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jiménez-García B; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., van Noort CW; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Honorato RV; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Bonvin AMJJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Wodak SJ; VIB Structural Biology Research Center, VUB, Brussels, Belgium.

المصدر: Proteins [Proteins] 2019 Dec; Vol. 87 (12), pp. 1200-1221. Date of Electronic Publication: 2019 Oct 25.

نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: MEDLINE

مواضيع طبية MeSH: Computational Biology* , Protein Conformation* , Software*, Proteins/*ultrastructure, Algorithms ; Binding Sites/genetics ; Databases, Protein ; Models, Molecular ; Protein Binding/genetics ; Protein Interaction Mapping ; Proteins/chemistry ; Proteins/genetics ; Structural Homology, Protein

المؤلفون: Kurkcuoglu Z; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Koukos PI; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Citro N; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Trellet ME; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Rodrigues JPGLM; James H. Clark Center, Stanford University, 318 Campus Drive, S210, Stanford, CA, 94305, USA., Moreira IS; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands.; CNC - Center for Neuroscience and Cell Biology, FMUC, Universidade de Coimbra, Rua Larga, Polo I, 1ºandar, 3004-517, Coimbra, Portugal., Roel-Touris J; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Melquiond ASJ; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Geng C; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Schaarschmidt J; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Xue LC; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Vangone A; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands., Bonvin AMJJ; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl.

المصدر: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2018 Jan; Vol. 32 (1), pp. 175-185. Date of Electronic Publication: 2017 Aug 22.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Springer Country of Publication: Netherlands NLM ID: 8710425 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1573-4951 (Electronic) Linking ISSN: 0920654X NLM ISO Abbreviation: J Comput Aided Mol Des Subsets: MEDLINE

مواضيع طبية MeSH: Drug Discovery* , Molecular Docking Simulation* , Software*, Receptors, Cytoplasmic and Nuclear/*metabolism, Binding Sites ; Computer-Aided Design ; Crystallography, X-Ray ; Drug Design ; Humans ; Ligands ; Protein Binding ; Protein Conformation ; Receptors, Cytoplasmic and Nuclear/agonists ; Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors ; Receptors, Cytoplasmic and Nuclear/chemistry ; Thermodynamics

المؤلفون: Vangone A; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Rodrigues JPGLM; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Xue LC; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., van Zundert GCP; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Geng C; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Kurkcuoglu Z; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Nellen M; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Narasimhan S; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Karaca E; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., van Dijk M; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Melquiond ASJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Visscher KM; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Trellet M; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Kastritis PL; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands., Bonvin AMJJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands.

المصدر: Proteins [Proteins] 2017 Aug; Vol. 85 (8), pp. 1589-1590.

نوع المنشور: Journal Article; Published Erratum

بيانات الدورية: Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8700181 Publication Model: Print Cited Medium: Internet ISSN: 1097-0134 (Electronic) Linking ISSN: 08873585 NLM ISO Abbreviation: Proteins Subsets: PubMed not MEDLINE

المؤلفون: van Zundert GCP; Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands., Rodrigues JPGLM; Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands., Trellet M; Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France., Schmitz C; Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia., Kastritis PL; European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Karaca E; European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany., Melquiond ASJ; Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands., van Dijk M; Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands., de Vries SJ; Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany., Bonvin AMJJ; Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands.

المصدر: Journal of molecular biology [J Mol Biol] 2016 Feb 22; Vol. 428 (4), pp. 720-725. Date of Electronic Publication: 2015 Sep 26.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

مواضيع طبية MeSH: Computational Biology/*methods , Macromolecular Substances/*chemistry , Molecular Biology/*methods, Internet

المؤلفون: van Zundert GCP; Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht 3584CH, the Netherlands., Melquiond ASJ; Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht 3584CH, the Netherlands., Bonvin AMJJ; Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht 3584CH, the Netherlands. Electronic address: a.m.j.j.bonvin@uu.nl.

المصدر: Structure (London, England : 1993) [Structure] 2015 May 05; Vol. 23 (5), pp. 949-960. Date of Electronic Publication: 2015 Apr 23.

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Cell Press Country of Publication: United States NLM ID: 101087697 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-4186 (Electronic) Linking ISSN: 09692126 NLM ISO Abbreviation: Structure Subsets: MEDLINE

مواضيع طبية MeSH: Computational Biology/*methods , Multiprotein Complexes/*chemistry , Multiprotein Complexes/*metabolism, Cryoelectron Microscopy ; Databases, Protein ; Models, Molecular ; Molecular Docking Simulation ; User-Computer Interface